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Protein engineering

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https://www.readbyqxmd.com/read/28732052/protein-asparagine-deamidation-prediction-based-on-structures-with-machine-learning-methods
#1
Lei Jia, Yaxiong Sun
Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein "hotspots" are amino acid residues that are subject to various chemical modifications, including deamidation, isomerization, glycosylation, oxidation etc. A more accurate prediction method for potential hotspot residues would allow their elimination or reduction as early as possible in the drug discovery process. In this work, we focus on prediction models for asparagine (Asn) deamidation...
2017: PloS One
https://www.readbyqxmd.com/read/28731580/rewiring-the-glucose-transportation-and-central-metabolic-pathways-for-overproduction-of-n-acetylglucosamine-in-bacillus-subtilis
#2
Yang Gu, Jieying Deng, Yanfeng Liu, Jianghua Li, Hyun-Dong Shin, Guocheng Du, Jian Chen, Long Liu
N-acetylglucosamine (GlcNAc) is an important amino sugar extensively used in the healthcare field. in a previous study, we constructed the recombinant Bacillus subtilis strain BSGN6-PxylA -glmS-pP43NMK-GNA1 (BN0-GNA1) for microbial production of GlcNAc by pathway design and modular optimization. Here, we further improved the production of GlcNAc by rewiring both the glucose transportation and central metabolic pathways. First, the phosphotransferase system (PTS) was blocked by deletion of three genes, yyzE (encoding the PTS system transporter subunit iiA YyzE), ypqE (encoding the PTS system transporter subunit iiA YpqE), and ptsG (encoding the PTS system glucose-specific EiiCBA component), resulting in 47...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731533/improvement-of-d-lactic-acid-production-in-saccharomyces-cerevisiae-under-acidic-conditions-by-evolutionary-and-rational-metabolic-engineering
#3
Seung-Ho Baek, Eunice Y Kwon, Sang-Jeong Bae, Bo-Ram Cho, Seon-Young Kim, Ji-Sook Hahn
Microbial lactic acid (LA) production under acidic fermentation conditions is favorable to reduce the production cost, but circumventing LA toxicity is a major challenge. We generated D-LA-producing Saccharomyces cerevisiae strain JHY5610 by expressing D-lactate dehydrogenase gene (Lm. ldhA) from Leuconostoc mesenteroides, while deleting genes involved in ethanol production (ADH1, ADH2, ADH3, ADH4, and ADH5), glycerol production (GPD1 and GPD2), and degradation of D-LA (DLD1). Adaptive laboratory evolution of JHY5610 led to a strain JHY5710 having higher LA tolerance and D-LA-production capability...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731528/improving-succinate-productivity-by-engineering-a-cyanobacterial-co2-concentrating-system-ccm-in-escherichia-coli
#4
Mengyong Xiao, Xinna Zhu, Changhao Bi, Yanhe Ma, Xueli Zhang
Biologically fixation of CO2 has great potential as a significant carbon source for biosynthesis, which is also a major way to reduce CO2 accumulation in atmosphere. Phosphoenolpyruvate (PEP) carboxylation is the key step of anaerobic succinate production in Escherichia coli. In this reaction, one mole CO2 is assimilated with PEP to form oxaloacetate by PEP carboxykinase (PCK). The preferred substrate of PCK is CO2 , which is very limited in cytoplasm. In this study, the carbon concentration mechanism (CCM) of cyanobacteria was introduced into E...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731353/altering-dna-programmable-colloidal-crystallization-paths-by-modulating-particle-repulsion
#5
Mary X Wang, Jeffrey D Brodin, Jaime A Millan, Soyoung E Seo, Martin Girard, Monica Olvera de la Cruz, Byeongdu Lee, Chad A Mirkin
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior...
July 21, 2017: Nano Letters
https://www.readbyqxmd.com/read/28731222/bio-nano-interface-and-environment-a-critical-review
#6
Gerardo Pulido-Reyes, Francisco Leganes, Francisca Fernández-Piñas, Roberto Rosal
The Bio-Nano interface is the boundary where the Engineered NanoMaterials (ENM) meet the biological system, exerting the biological function for what they have been designed or inducing adverse effects to other cells or organisms when they reach non-target scenarios, i.e: the natural environment. Research has been performed to determine the fate, transport, and toxic properties of ENM, but much of it focused on pristine or "as manufactured" ENM or where modifications of the materials were not assessed. This article reviews the most recent progresses regarding the Bio-Nano interface and the transformations that ENM suffer in the environment, paying special attention to the adsorption of environmental biomolecules on the surface of ENM...
July 21, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28730473/expression-of-recombinant-phosphoproteins-for-signal-transduction-studies
#7
Karl W Barber, Jesse Rinehart
Complex signaling cascades are difficult to study in vitro without phosphorylated proteins. Here, we describe a technique for the routine production of recombinant phosphoproteins by directly incorporating phosphoserine as a nonstandard amino acid. This protocol utilizes an optimized phosphoserine orthogonal translation system and an engineered strain of E. coli containing no genomic amber codons. This approach has been used to generate a variety of phosphorylated proteins to understand the role of protein phosphorylation in cell signaling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730450/crispr-cas-rna-scaffolds-for-transcriptional-programming-in-yeast
#8
Jesse G Zalatan
CRISPR scaffold RNAs (scRNAs) provide a modular system for locus-specific transcriptional programming. scRNAs are generated by extending CRISPR guide RNA sequences with domains that recruit RNA-binding proteins, thus physically linking DNA binding and protein recruitment activities. A single scRNA molecule encodes information about the target locus and instructions about what regulatory function to execute at that locus. Sets of scRNA constructs can be used to generate synthetic multigene transcriptional programs in which some genes are activated and others are repressed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729884/genome-wide-landscape-of-position-effects-on-heterogeneous-gene-expression-in-saccharomyces-cerevisiae
#9
Xiao-Le Wu, Bing-Zhi Li, Wen-Zheng Zhang, Kai Song, Hao Qi, Jun-Biao Dai, Ying-Jin Yuan
BACKGROUND: Integration of heterogeneous genes is widely applied in synthetic biology and metabolic engineering. However, knowledge about the effect of integrative position on gene expression remains limited. RESULTS: We established a genome-wide landscape of position effect on gene expression in Saccharomyces cerevisiae. The expression cassette of red fluorescence protein (RFP) gene was constructed and inserted at 1044 loci, which were scattered uniformly in the yeast genome...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28729758/analysis-of-correlated-mutations-in-ras-g-domain
#10
Ekta Pathak
Ras GTPases are most prevalent proto-oncogenes in human cancer. Mutations in Ras remain untreatable more than three decades after the initial discovery. At the amino acid level, some residues under physical or functional constraints exhibit correlated mutations also known as coevolving/covariant residues. Revealing intra-molecular co-evolution between amino acid sites of proteins has become an emerging area of research as it enlightens the importance of variable regions. Here, I have identified and analyzed the coevolving residues in the Ras GTP binding domain (G-domain)...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729713/tunable-uptake-release-mechanism-of-protein-microgel-particles-in-biomimicking-environment
#11
A Pepe, P Podesva, G Simone
Microgels are intra-molecular crosslinked macromolecules that can be used as vehicles to deliver and release drugs at the point-of-need in the patient's body. Here, gelatin microgels were formed from microfluidics droplets, stabilised by aldehydes and frozen into a spheroidal shape. Microgel morphology and response to external stimuli were characterised. It was found that the behaviour of the spheroidal microgels was sensitive to both pH and ionic strength and that the distribution of charges into the microgels affected the behaviour of swelling and uptake...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729665/identification-of-proteins-that-specifically-recognize-and-bind-protofibrillar-aggregates-of-amyloid-%C3%AE
#12
Elisabet Wahlberg, M Mahafuzur Rahman, Hanna Lindberg, Elin Gunneriusson, Benjamin Schmuck, Christofer Lendel, Mats Sandgren, John Löfblom, Stefan Ståhl, Torleif Härd
Protofibrils of the 42 amino acids long amyloid-β peptide are transient pre-fibrillar intermediates in the process of peptide aggregation into amyloid plaques and are thought to play a critical role in the pathology of Alzheimer's disease. Hence, there is a need for research reagents and potential diagnostic reagents for detection and imaging of such aggregates. Here we describe an in vitro selection of Affibody molecules that bind to protofibrils of Aβ42cc, which is a stable engineered mimic of wild type Aβ42 protofibrils...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727740/genetically-engineered-suicide-gene-in-mesenchymal-stem-cells-using-a-tet-on-system-for-anaplastic-thyroid-cancer
#13
Senthilkumar Kalimuthu, Ji Min Oh, Prakash Gangadaran, Liya Zhu, Ho Won Lee, Yong Hyun Jeon, Shin Young Jeong, Sang-Woo Lee, Jaetae Lee, Byeong-Cheol Ahn
Anaplastic thyroid cancer (ATC) is the most aggressive malignancy of the thyroid, during which undifferentiated tumors arise from the thyroid follicular epithelium. ATC has a very poor prognosis due to its aggressive behavior and poor response to conventional therapies. Gene-directed enzyme/prodrug therapy using genetically engineered mesenchymal stromal cells (MSC) is a promising therapeutic strategy. The doxycycline (DOX)-controlled Tet inducible system is the most widely utilized regulatory system and could be a useful tool for therapeutic gene-based therapies...
2017: PloS One
https://www.readbyqxmd.com/read/28727448/extensive-survey-of-antibody-invariant-positions-for-efficient-chemical-conjugation-using-expanded-genetic-codes
#14
Akifumi Kato, Mitsuo Kuratani, Tatsuo Yanagisawa, Kazumasa Ohtake, Akiko Hayashi, Yoshimi Amano, Kaname Kimura, Shigeyuki Yokoyama, Kensaku Sakamoto, Yasuhisa Shiraishi
The site-specific chemical conjugation of proteins, following synthesis with an expanded genetic code, promises to advance antibody-based technologies, including antibody drug conjugation and the creation of bispecific Fab dimers. The incorporation of non-natural amino acids into antibodies not only guarantees site specificity but also allows the use of bio-orthogonal chemistry. However, the efficiency of amino acid incorporation fluctuates significantly among different sites, thereby hampering the identification of useful conjugation sites...
July 20, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28727145/transcriptional-control-of-photosynthetic-capacity-conservation-and-divergence-from-arabidopsis-to-rice
#15
REVIEW
Peng Wang, Ross-William Hendron, Steven Kelly
1 I. 1 II. 2 III. 5 IV. 10 12 References 12 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression...
July 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28727079/detection-of-dietary-dna-protein-and-glyphosate-in-meat-milk-and-eggs
#16
A L Van Eenennaam, A E Young
Products such as meat, milk, and eggs from animals that have consumed genetically engineered (GE) feed are not currently subject to mandatory GE labeling requirements. Some voluntary "non-genetically modified organism" labeling has been associated with such products, indicating that the animals were not fed GE crops, as there are no commercialized GE food animals. This review summarizes the available scientific literature on the detection of dietary DNA and protein in animal products and briefly discusses the implications of mandatory GE labeling for products from animals that have consumed GE feed...
July 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726876/bioceramic-nanocomposite-thiol-acrylate-polyhipe-scaffolds-for-enhanced-osteoblastic-cell-culture-in-3d
#17
Aaron Lee, Caitlin R Langford, Luis M Rodriguez-Lorenzo, Helmut Thissen, Neil R Cameron
Emulsion-templated (polyHIPE) scaffolds for bone tissue engineering were produced by photopolymerisation of a mixture of trimethylolpropane tris(3-mercaptopropionate) and dipentaerythritol penta-/hexa-acrylate in the presence of hydroxyapatite (HA) or strontium-modified hydroxyapatite (SrHA) nanoparticles. Porous and permeable polyHIPE materials were produced regardless of the type or incorporation level of the bioceramic, although higher loadings resulted in a larger average pore diameter. Inclusion of HA and SrHA into the scaffolds was confirmed by EDX-SEM, FTIR and XPS and quantified by thermogravimetry...
July 20, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28726576/recent-developments-in-thiolated-polymeric-hydrogels-for-tissue-engineering-applications
#18
Mani Gajendiran, Jae-Sung Rhee, Kyobum Kim
This review focuses on the recent strategy in the preparation of thiolated polymers and fabrication of their hydrogel matrices. The mechanism involved in the synthesis of thiolated polymers and fabrication of thiolated polymer hydrogels is exemplified with suitable schematic representations reported in the recent literature. The 2-iminothiolane namely "Traut's reagent" has been widely employed for effectively thiolating the natural polymers such as collagen and gelatin which contain free amino group in their back bone...
July 20, 2017: Tissue Engineering. Part B, Reviews
https://www.readbyqxmd.com/read/28726551/extracellular-matrix-and-integrin-expression-profiles-in-fuchs-endothelial-corneal-dystrophy-cells-and-tissue-model
#19
Benjamin Goyer, Mathieu Thériault, Sébastien P Gendron, Isabelle Brunette, Patrick J Rochette, Stéphanie Proulx
Primary corneal endothelial cell cultures and 3D engineered tissue models were used to study the aberrant deposition of extracellular matrix (ECM) in a vision impairing pathology known as Fuchs endothelial corneal dystrophy (FECD). Corneal endothelial cells (CEC) were isolated from excised Descemet membranes of patients with end-stage FECD. CEC isolated from healthy corneas served as controls. Microarray gene profiling was performed on post-confluent cultures of healthy and FECD cells. Protein expression analyses were conducted on tissue models that were engineered by seeding an endothelium on previously devitalized human stromal carriers...
July 20, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28726405/fluorescence-enhancement-of-unconstrained-gfp-chromophore-analogues-based-on-the-push-pull-substituent-effect
#20
Meng-Shiue Tsai, Chun-Lin Ou, Chi-Jui Tsai, Yen-Chin Huang, Yuan-Chung Cheng, Shih-Sheng Sun, Jye-Shane Yang
Unlike the high fluorescence quantum yield of the naturally occurring green fluorescence protein (GFP, Φf ∼ 0.8), the GFP chromophore, a benzylidenedimethylimidazolinone (BDI) dye, is nearly nonfluorescent (Φf < 0.001) in common solutions at room temperature. While many efforts have been devoted into the BDI chromophore engineering for fluorescence recovery, limited success has been achieved for structurally unconstrained GFP chromophore analogues (uGFPc). Herein we report a rational design of uGFPc toward an unprecedentedly high fluorescence quantum efficiency of 0...
July 20, 2017: Journal of Organic Chemistry
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