keyword
MENU ▼
Read by QxMD icon Read
search

Protein engineering

keyword
https://www.readbyqxmd.com/read/28231515/computational-tools-for-enzyme-improvement-why-everyone-can-and-should-use-them
#1
REVIEW
Maximilian Ccjc Ebert, Joelle N Pelletier
This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists...
February 20, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28231445/principles-of-systems-biology-no-14
#2
(no author information available yet)
This month: sage advice from phage to their offspring; systematic analyses of protein quality control, mitochondrial respiration, and woody biomass; a continental-scale experiment; and engineered protein tools galore.
February 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28231413/metabolic-chemical-reporters-of-glycans-exhibit-cell-type-selective-metabolism-and-glycoprotein-labeling
#3
Anna R Batt, Balyn W Zaro, Marisol X Navarro, Matthew Robert Pratt
Since the pioneering work by Reutter and co-workers that demonstrated structural flexibility in the carbohydrate biosynthesis and glycosylation pathways, many different labs have used unnatural monosaccharide analogs to perform glycan engineering on the surface of living cells. A subset of these unnatural monosaccharides contain bioorthogonal groups that enable the selective installation of visualization or enrichment tags. These metabolic chemical reporters (MCRs) have proven to be powerful for the unbiased identification of glycoproteins; however they do have certain limitations...
February 23, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28231264/precision-engineering-for-prrsv-resistance-in-pigs-macrophages-from-genome-edited-pigs-lacking-cd163-srcr5-domain-are-fully-resistant-to-both-prrsv-genotypes-while-maintaining-biological-function
#4
Christine Burkard, Simon G Lillico, Elizabeth Reid, Ben Jackson, Alan J Mileham, Tahar Ait-Ali, C Bruce A Whitelaw, Alan L Archibald
Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28230992/novel-design-of-heptad-amphiphiles-to-enhance-cell-selectivity-salt-resistance-anti-biofilm-properties-and-their-membrane-disruptive-mechanism
#5
Xiujing Dou, Xin Zhu, Jiajun Wang, Na Dong, Anshan Shan
Coiled-coil, a basic folding pattern of native proteins, was previously demonstrated to be associated with the specific spatial recognition, association, and dissociation of proteins and can be used to perfect engineering peptide model. Thus, in this study, a series of amphiphiles composed of heptads repeats with coiled-coil structures was constructed, and the designed peptides exhibited a broad spectrum of antimicrobial activities. Circular dichroism and biological assays showed that the heptad repeats and length of the linker between the heptads largely influenced the amphiphile's helical propensity and cell selectivity...
February 23, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28230977/extracellular-self-assembly-of-functional-and-tunable-protein-conjugates-from-bacillus-subtilis
#6
Charlie Gilbert, Mark Howarth, Colin R Harwood, Tom Ellis
The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically-encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis...
February 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28230927/crispr-cas9-technologies
#7
Bart O Williams, Matthew L Warman
The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) pathway is revolutionizing biological research. Modifications to this primitive prokaryotic immune system now enable scientists to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms. Thus, many laboratories can now perform important experiments that previously were considered scientifically risky or too costly. Here, we describe the components of the CRISPR/Cas system that have been engineered for use in eukaryotes...
February 23, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28230321/disruption-of-genes-involved-in-corvet-complex-leads-to-enhanced-secretion-of-heterologous-carboxylesterase-only-in-protease-deficient-pichia-pastoris
#8
Lukas Marsalek, Clemens Gruber, Friedrich Altmann, Markus Aleschko, Diethard Mattanovich, Brigitte Gasser, Verena Puxbaum
The methylotrophic yeast Pichia pastoris (Komagataella spp.) is a popular microbial host for the production of recombinant proteins. Previous studies have shown that mis-sorting to the vacuole can be a bottleneck during production of recombinant secretory proteins in yeast, however, no information was available for P. pastoris. In this work we have therefore generated vps (vacuolar protein sorting) mutant strains disrupted in genes involved in the CORVET tethering complex at the early stages of endosomal sorting...
February 23, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28230065/in-vivo-evaluation-of-a-novel-format-of-a-bivalent-her3-targeting-and-albumin-binding-therapeutic-affibody-construct
#9
Tarek Z Bass, Maria Rosestedt, Bogdan Mitran, Fredrik Y Frejd, John Löfblom, Vladimir Tolmachev, Stefan Ståhl, Anna Orlova
Overexpression of human epidermal growth factor receptor 3 (HER3) is involved in resistance to several therapies for malignant tumours. Currently, several anti-HER3 monoclonal antibodies are under clinical development. We introduce an alternative approach to HER3-targeted therapy based on engineered scaffold proteins, i.e. affibody molecules. We designed a small construct (22.5 kDa, denoted 3A3), consisting of two high-affinity anti-HER3 affibody molecules flanking an albumin-binding domain ABD, which was introduced for prolonged residence in circulation...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230059/synergistic-effects-of-dimethyloxallyl-glycine-and-recombinant-human-bone-morphogenetic-protein-2-on-repair-of-critical-sized-bone-defects-in-rats
#10
Xin Qi, Yang Liu, Zhen-Yu Ding, Jia-Qing Cao, Jing-Huan Huang, Jie-Yuan Zhang, Wei-Tao Jia, Jing Wang, Chang-Sheng Liu, Xiao-Lin Li
In bone remodeling, osteogenesis is closely coupled to angiogenesis. Bone tissue engineering using multifunctional bioactive materials is a promising technique which has the ability to simultaneously stimulate osteogenesis and angiogenesis for repair of bone defects. We developed mesoporous bioactive glass (MBG)-doped poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) composite scaffolds as delivery vehicle. Two bioactive molecules, dimethyloxalylglycine (DMOG), a small-molecule angiogenic drug, and recombinant human bone morphogenetic protein-2 (rhBMP-2), an osteoinductive growth factor, were co-incorporated into the scaffold...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229928/an-expanded-genetic-code-for-probing-the-role-of-electrostatics-in-enzyme-catalysis-by-vibrational-stark-spectroscopy
#11
REVIEW
Jan-Stefan Völler, Hernan Biava, Peter Hildebrandt, Nediljko Budisa
BACKGROUND: To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW: This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS: ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics...
February 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28228595/hepatitis-c-virus-specific-t-cell-receptor-mrna-engineered-human-t-cells-impact-of-antigen-specificity-on-functional-properties
#12
Anangi Balasiddaiah, Haleh Davanian, Soo Aleman, Anna Pasetto, Lars Frelin, Matti Sällberg, Volker Lohmann, Sarene Koh, Antonio Bertoletti, Margaret Chen
Therapy with genetically modified autologous T cells has shown great promise in cancer therapy. For an efficient control of hepatitis C virus (HCV) infection, cytotoxic T cells (CTL) are pivotal but persistence of activated T cells may lead to liver toxicity. Here, anti-HCV T cell receptors (TCRs) recognising the HCV non-structural (NS) NS3 or NS5 viral peptide target were examined by mRNA transfection of human peripheral blood lymphocytes (PBL) derived from healthy donors as well as chronically infected HCV patients...
February 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28228592/functional-relevance-of-the-n-terminal-domain-of-pseudorabies-virus-envelope-glycoprotein-h-and-its-interaction-with-glycoprotein-l
#13
Melina Vallbracht, Sascha Rehwaldt, Barbara G Klupp, Thomas C Mettenleiter, Walter Fuchs
Several envelope glycoproteins are involved in herpesvirus entry into cells, direct cell-to-cell spread, and induction of cell fusion. The membrane fusion protein gB and the presumably gB-activating heterodimer gH/gL are essential for these processes and conserved throughout the Herpesviridae However, after extended cell culture passage of gL-negative mutants of the alphaherpesvirus pseudorabies virus (PrV) phenotypic revertants could be isolated which had acquired spontaneous mutations affecting the gL-interacting N-terminal part of the gH ectodomain (gDH, gH(B4...
February 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28228480/a-stable-but-reversible-integrated-surrogate-reporter-for-assaying-crispr-cas9-stimulated-homology-directed-repair
#14
Yahong Wen, Grace Liao, Thomas Pritchard, Ting-Ting Zhao, Jon P Connelly, Shondra M Pruett-Miller, Valerie Blanc, Nicholas O Davidson, Blair B Madison
The discovery and application of CRISPR/Cas9 technology for genome editing has greatly accelerated targeted mutagenesis in a variety of organisms. CRISPR/Cas9-mediated site-specific cleavage is typically exploited for the generation of insertions or deletions (indels) following aberrant dsDNA repair via the endogenous non-homology end-joining (NHEJ) pathway, or alternatively, for enhancing homology directed repair (HDR) to facilitate the generation of a specific mutation (or knock-in). However, there is a need for efficient cellular assays that can measure Cas9/guide RNA (gRNA) activity...
February 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28228478/an-engineered-tgf-%C3%AE-monomer-that-functions-as-a-dominant-negative-to-block-tgf-%C3%AE-signaling
#15
Sun Kyung Kim, Lindsey Barron, Cynthia S Hinck, Elyse M Petrunak, Kristin E Cano, Avinash Thangirala, Brian Iskra, Molly Brothers, Machell Vonberg, Belinda Leal, Blair Richter, Ravindra Kodali, Alex B Taylor, Shoucheng Du, Christopher O Barnes, Traian Sulea, Guillermo Calero, P John Hart, Matthew J Hart, Borries Demeler, Andrew P Hinck
The transforming growth factor beta isoforms, TGF-β1, -β2, and -β3 are small secreted homodimeric signaling proteins with essential roles in regulating the adaptive immune system and maintaining the extracellular matrix. However, dysregulation of the TGF-β pathway is responsible for promoting the progression of several human diseases, including cancer and fibrosis. In spite of the known importance of TGF-βs in promoting disease progression, no inhibitors have been approved for use in humans. Herein, we describe an engineered TGF-β monomer, lacking the heel helix, a structural motif essential for binding the TGF-β type I receptor, TβRI, but dispensible for binding the other receptor required for TGF-β signaling, the TGF-β type II receptor, TβRII, as an alternative therapeutic modality for blocking TGF-β signaling in humans...
February 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28227432/colony-size-effect-on-neural-differentiation-of-embryonic-stem-cells-microprinted-on-stromal-cells
#16
Ramila Joshi, James Buchanan, Hossein Tavana, Ramila Joshi, James Buchanan, Hossein Tavana, Ramila Joshi, James Buchanan, Hossein Tavana
Controlling cellular microenvironment to induce neural differentiation of embryonic stem cells (ESCs) remains a major challenge. We address this need by introducing a micro-engineered co-culture system that resembles embryonic development in terms of direct intercellular interactions and induces neural differentiation of ESCs. A polymeric aqueous two-phase system (ATPS)-mediated robotic microprinting technology allows precise localization of mouse ESCs (mESCs) over a layer of supporting stromal cells. mESCs proliferate over a 2-week culture period into a single colony of defined size...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226291/cell-free-synthetic-biology-for-environmental-sensing-and-remediation
#17
REVIEW
David K Karig
The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications...
February 19, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28225593/programmed-self-assembly-of-hierarchical-nanostructures-through-protein-nanoparticle-co-engineering
#18
Rubul Mout, Gulen Yesilbag Tonga, Li-Sheng Wang, Moumita Ray, Trinava Roy, Vincent M Rotello
Hierarchical organization of macromolecules through self-assembly is a prominent feature in biological systems. Synthetic fabrication of such structures provides materials with emergent functions. Here we report the fabrication of self-assembled superstructures through co-engineering of recombinant proteins and nanoparticles. These structures feature a highly-sophisticated level of multi-layered hierarchical organization of the components: individual proteins and nanoparticles co-assemble to form discrete assemblies that collapse to form granules, which then further self-organize to generate superstructures of hundreds of nanometer size...
February 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28225583/microfluidic-encapsulation-of-human-mesenchymal-stem-cells-for-articular-cartilage-tissue-regeneration
#19
Fanyi Li, Vinh X Truong, Helmut Thissen, Jessica Frith, John S Forsythe
Stem cell injections for the treatment of articular cartilage damage are a promising approach to achieve tissue regeneration. However, this method is encumbered by high cell apoptosis rates, low retention in the cartilage lesion and inefficient chondrogenesis. Here, we have used a facile, very low cost-based microfluidic technique to create visible light-cured hydrogel microparticles composed of gelatin norbornene (GelNB) and a polyethylene glycol (PEG) crosslinker. In addition, we have demonstrated that the process enables the rapid in situ micro-encapsulation of human bone marrow-derived mesenchymal stem cells (hBMSCs) under biocompatible microfluidic-processing conditions for long-term maintenance...
February 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28225256/analysis-and-control-of-chain-mobility-in-protein-hydrogels
#20
Peter B Rapp, Ahmad K Omar, Jeff J Shen, Maren E Buck, Zhen-Gang Wang, David A Tirrell
Coiled-coil domains can direct the assembly of protein block copolymers into physically crosslinked, viscoelastic hydrogels. Here we describe the use of fluorescence recovery after photobleaching (FRAP) to probe chain mobility in reversible hydrogels assembled from engineered proteins bearing terminal coiled-coil domains. We show that chain mobility can be related to the underlying dynamics of the coiled-coil domains by application of a 3-state "hopping" model of chain migration. We further show that genetic programming allows the effective mobility of network chains to be varied 500-fold through modest changes in protein sequence...
February 22, 2017: Journal of the American Chemical Society
keyword
keyword
10234
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"