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Protein engineering

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https://www.readbyqxmd.com/read/29166564/optical-control-of-dopamine-receptors-using-a-photoswitchable-tethered-inverse-agonist
#1
Prashant Donthamsetti, Nils Winter, Matthias Schönberger, Joshua Levitz, Cherise Stanley, Jonathan A Javitch, Ehud Y Isacoff, Dirk Trauner
Family A G protein-coupled receptors (GPCRs) control diverse biological processes and are of great clinical relevance. Their archetype rhodopsin becomes naturally light sensitive by binding covalently to the photoswitchable tethered ligand (PTL) retinal. Other GPCRs, however, neither bind covalently to ligands nor are light sensitive. We sought to impart the logic of rhodopsin to light-insensitive Family A GPCRs in order to enable their remote control in a receptor-specific, cell-type-specific and spatio-temporally precise manner...
November 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29166010/conformational-dynamics-of-asparagine-at-coiled-coil-interfaces
#2
Franziska Thomas, Ai Niitsu, Alain Oregioni, Gail J Bartlett, Derek N Woolfson
Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds or not...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29165861/engineered-biomolecular-recognition-of-rdx-using-a-thermostable-alcohol-dehydrogenase-as-a-protein-scaffold
#3
Beyza Bulutoglu, Jennifer Haghpanah, Elliot Campbell, Scott A Banta
There are many biotechnology applications that would benefit from simple, stable proteins with engineered biomolecular recognition. Here we explored the hypothesis that a thermostable alcohol dehydrogenase (AdhD from P. furisosus) could be engineered to bind a small molecule instead of a cofactor or molecules involved in the catalytic transition state. We chose the explosive molecule 1,3,5-trinitro-1,3,5-triazine (RDX) as a proof-of-concept. Its low solubility in water was exploited for immobilization for biopanning using ribosome display...
November 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29164963/amorphous-silica-nanoparticles-induce-malignant-transformation-and-tumorigenesis-of-human-lung-epithelial-cells-via-p53-signaling
#4
Caixia Guo, Ji Wang, Man Yang, Yang Li, Shuxiang Cui, Xianqing Zhou, Yanbo Li, Zhiwei Sun
Rapid development and deployment of engineered nanomaterials, such as amorphous silica nanoparticles (SiNPs) in various commercial and biomedical applications have raised concerns about their potential adverse health effects, especially their chronic effects which have not been well addressed. In this study, human lung epithelial cells, BEAS-2B were continuously exposed to amorphous SiNPs, 5 μg/mL for 40 passages. We demonstrated here that prolonged exposure of BEAS-2B cells to amorphous SiNPs induced malignant transformation as indicated by enhanced cellular proliferation, anchorage-independent cell growth, and increased cell migration...
November 22, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29164876/live-cell-imaging-of-endogenous-rnas-using-pumilio-homology-domain-mutants-principles-and-applications
#5
Hideaki Yoshimura
Recently, dynamic changes in RNA location in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescence labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction to cells and transgenic organisms in cell type and tissue specific manner by genetic engineering techniques...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29164819/decellularized-bovine-cotyledons-may-serve-as-biological-scaffolds-with-preserved-vascular-arrangement
#6
Rodrigo da Silva Nunes Barreto, Patricia Romagnolli, Andrea Maria Mess, Maria Angelica Miglino
Technically produced scaffolds are common to establish transplantable tissues for Regenerative Medicine, but also biological ones that are closer to the natural condition become of interest. Placentas are promising, because they represented available, complete organs with rich extracellular matrix (ECM) and well developed vasculature that easily could build anastomoses to a host´s organ. Only placentas from larger animal models such as the bovine meet the dimensions large enough for most organs, but are not adequately described yet...
November 21, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29164808/a-universal-approach-to-correct-various-hbb-gene-mutations-in-human-stem-cells-for-gene-therapy-of-beta-thalassemia-and-sickle-cell-disease
#7
Liuhong Cai, Hao Bai, Vasiliki Mahairaki, Yongxing Gao, Chaoxia He, Yanfei Wen, You-Chuan Jin, You Wang, Rachel L Pan, Armaan Qasba, Zhaohui Ye, Linzhao Cheng
Beta-thalassemia is one of the most common recessive genetic diseases, caused by mutations in the HBB gene. Over 200 different types of mutations in the HBB gene containing three exons have been identified in patients with β-thalassemia (β-thal) whereas a homozygous mutation in exon 1 causes sickle cell disease (SCD). Novel therapeutic strategies to permanently correct the HBB mutation in stem cells that are able to expand and differentiate into erythrocytes producing corrected HBB proteins are highly desirable...
November 21, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29164771/functional-self-assembled-peptide-scaffold-inhibits-tnf-alpha-induced-inflammation-and-apoptosis-in-nucleus-pulposus-cells-by-suppressing-nf-%C3%AE%C2%BAb-signaling
#8
Xiaochuan Li, Shi Cheng, Yaohong Wu, Jingwei Ying, Chaofeng Wang, Tianyong Wen, Xuedong Bai, Wei Ji, Deli Wang, Dike Ruan
Although nucleus pulposus (NP) tissue engineering has achieved tremendous success, researches still face the huge obstacles in maintaining cell survival and function. A novel functional self-assembled peptide RADA-KPSS was constructed by conjugating BMP-7 short active fragment (KPSS) to the C-terminus of RADA16-I that displays anti-inflammatory and anti-apoptosis effects. However, whether this functional self-assembled RADA-KPSS peptide can alleviate inflammation and NPC apoptosis induced by TNF-α has not been studied...
November 22, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/29163920/harnessing-fungal-nonribosomal-cyclodepsipeptide-synthetases-for-mechanistic-insights-and-tailored-engineering
#9
Charlotte Steiniger, Sylvester Hoffmann, Andi Mainz, Marcel Kaiser, Kerstin Voigt, Vera Meyer, Roderich D Süssmuth
Nonribosomal peptide synthetases represent potential platforms for the design and engineering of structurally complex peptides. While previous focus has been centred mainly on bacterial systems, fungal synthetases assembling drugs like the antifungal echinocandins, the antibacterial cephalosporins or the anthelmintic cyclodepsipeptide (CDP) PF1022 await in-depth exploitation. As various mechanistic features of fungal CDP biosynthesis are only partly understood, effective engineering of NRPSs has been severely hampered...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29163527/engineered-tolerance-tailoring-development-function-and-antigen-specificity-of-regulatory-t-cells
#10
REVIEW
Nicholas A J Dawson, Jens Vent-Schmidt, Megan K Levings
Regulatory T cells (Tregs) are potent suppressors of immune responses and are currently being clinically tested for their potential to stop or control undesired immune responses in autoimmunity, hematopoietic stem cell transplantation, and solid organ transplantation. Current clinical approaches aim to boost Tregs in vivo either by using Treg-promoting small molecules/proteins and/or by adoptive transfer of expanded Tregs. However, the applicability of Treg-based immunotherapies continues to be hindered by technical limitations related to cell isolation and expansion of a pure, well-characterized, and targeted Treg product...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163459/crispr-cas9-system-as-a-valuable-genome-editing-tool-for-wine-yeasts-with-application-to-decrease-urea-production
#11
Ileana Vigentini, Marinella Gebbia, Alessandra Belotti, Roberto Foschino, Frederick P Roth
An extensive repertoire of molecular tools is available for genetic analysis in laboratory strains of S. cerevisiae. Although this has widely contributed to the interpretation of gene functionality within haploid laboratory isolates, the genetics of metabolism in commercially-relevant polyploid yeast strains is still poorly understood. Genetic engineering in industrial yeasts is undergoing major changes due to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) engineering approaches...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163080/behavioral-and-neurochemical-phenotyping-of-mice-incapable-of-homer1a-induction
#12
Michael C Datko, Jia-Hua Hu, Melanie Williams, Cindy M Reyes, Kevin D Lominac, Georg von Jonquieres, Matthias Klugmann, Paul F Worley, Karen K Szumlinski
Immediate early and constitutively expressed products of the Homer1 gene regulate the functional assembly of post-synaptic density proteins at glutamatergic synapses to influence excitatory neurotransmission and synaptic plasticity. Earlier studies of Homer1 gene knock-out (KO) mice indicated active, but distinct, roles for IEG and constitutively expressed Homer1 gene products in regulating cognitive, emotional, motivational and sensorimotor processing, as well as behavioral and neurochemical sensitivity to cocaine...
2017: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/29162107/production-of-highly-efficient-cellulase-mixtures-by-genetically-exploiting-the-potentials-of-trichoderma-reesei-endogenous-cellulases-for-hydrolysis-of-corncob-residues
#13
Yuanchao Qian, Lixia Zhong, Jia Gao, Ningning Sun, Yifan Wang, Guoyong Sun, Yinbo Qu, Yaohua Zhong
BACKGROUND: Trichoderma reesei is one of the most important fungi utilized for cellulase production. However, its cellulase system has been proven to be present in suboptimal ratio for deconstruction of lignocellulosic substrates. Although previous enzymatic optimization studies have acquired different types of in vitro synthetic mixtures for efficient lignocellulose hydrolysis, production of in vivo optimized cellulase mixtures by industrial strains remains one of the obstacles to reduce enzyme cost in the biofuels production from lignocellulosic biomass...
November 21, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29161434/designing-a-mutant-candida-uricase-with-improved-polymerization-state-and-enzymatic-activity
#14
Lei Tao, Dandan Li, Yonghong Li, Xinchang Shi, Junzhi Wang, Chunming Rao, Yingqi Zhang
As human uricase has been silenced during evolution, counterparts from other species become an alternative for the treatment of hyperuricemia. Candida uricase is a promising option among them, but its aggregation propensity remains a major obstacle to clinical use. In this study, we designed two mutations according to homology-modeled 3D structure of Candida uricase: Cys249Ser substitution and C-terminal Leu deletion. The wild-type uricase and three mutants containing either or both of the mutations were expressed in Escherichiacoli BL21 and validated by mass spectrometry...
November 17, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29161022/structural-and-functional-studies-of-the-daunorubicin-priming-ketosynthase-dpsc
#15
David R Jackson, Gaurav Shakya, Avinash B Patel, Lina Y Mohammed, Kostas Vasilakis, Pakorn Wattana-Amorn, Timothy R Valentic, Jacob Milligan, Matthew P Crump, John Crosby, Shiou-Chuan Tsai
Daunorubicin is a type II polyketide, one of a large class of polyaromatic natural products with anticancer, antibiotic and antiviral activity. Type II polyketides are formed by the assembly of malonyl-CoA building blocks, though in rare cases, biosynthesis is initiated by the incorporation of a non-malonyl derived starter unit, which adds molecular diversity to the poly-β-ketone backbone. Priming mechanisms for the transfer of novel starter units onto polyketide synthases (PKS) are still poorly understood...
November 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29161017/detecting-interactions-between-nanomaterials-and-cell-membranes-by-synthetic-nanopores
#16
Binquan Luan, Shuo Zhou, Deqiang Wang, Ruhong Zhou
Engineered nanomaterials have been increasingly utilized in industry for various consumer products, environment treatments, energy storages and biomedical applications. Meanwhile, it has been established that certain nanomaterials can be toxic to biological cells from extensive experimental and theoretical studies. Despite that the exact molecular mechanisms of these nanomaterials' toxicity are still not well understood, it is ubiquitous that their interactions with cell membranes, through either endocytosis or penetration (and thus potential lysis), act as the first step towards the inflammation or even the death of a cell...
November 21, 2017: ACS Nano
https://www.readbyqxmd.com/read/29161010/emerging-approaches-for-spatiotemporal-control-of-targeted-genome-with-inducible-crispr-cas9
#17
Yuta Nihongaki, Takahiro Otabe, Moritoshi Sato
The breakthrough CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) nuclease has revolutionized our ability in genome engineering. Although Cas9 is already a powerful tool for simple and efficient target endogenous gene manipulation, further engineering of Cas9 will improve the performance of Cas9, such as gene-editing efficiency and accuracy in vivo, and expand the application possibility of this Cas9 technology. The emerging inducible Cas9 methods, which can control the activity of Cas9 using an external stimulus such as chemicals and light, have the potential to provide spatiotemporal gene manipulation in user-defined cell population at a specific time and improve the accuracy of Cas9-mediated genome editing...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29160940/morphological-transformation-of-hbmsc-from-2d-monolayer-to-3d-microtissue-on-low-crystallinity-sf-pcl-patch-with-promotion-of-cardiomyogenesis
#18
Hsin-Yu Lo, An-Li Huang, Pei-Chi Lee, Tze-Wen Chung, Shoei-Shen Wang
The effects of the stiffness of substrates on the cell behaviors of hBMSC have been investigated but the effects of the secondary structures of proteins in the substrates on the morphological transformation and differentiation of hBMSC have yet been elucidated. To investigate these issues, SP cardiac patches of poly(ε-caprolactone) (P), on which is grafted by silk (SF) with various β-sheet contents (or crystallinity) to provide various degrees of stiffness, were produced to examine the in-vitro behaviors of hBMSC during proliferation, and cardiomyogenesis on the SP patches...
November 21, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29160870/engineering-high-performance-hairpin-stacking-circuits-for-logic-gate-operation-and-highly-sensitive-biosensing-assay-of-microrna
#19
Yueli Xing, Xinmin Li, Taixian Yuan, Wei Cheng, Dandan Li, Tianxiao Yu, Xiaojuan Ding, Shijia Ding
Recently, hairpin stacking circuits (HSC) based on toehold-mediated strand displacement have been engineered to detect nucleic acids and proteins. However, the three metastable hairpins in a HSC system can potentially react non-specifically in the absence of a catalyst, limiting its practical application. Here, we developed a unique hairpin design guideline to eliminate circuit leakage of HSC, and the high-performance HSC was successfully implemented on logic gate building and biosensing. We began by analyzing the sources of circuit leakage and optimizing the toehold lengths of hairpins in the HSC system based on the surface plasmon resonance (SPR) technique...
November 21, 2017: Analyst
https://www.readbyqxmd.com/read/29160592/sugar-flux-and-signaling-in-plant-microbe-interactions
#20
Margaret Bezrutczyk, Jungil Yang, Joon-Seob Eom, Matthew Prior, Davide Sosso, Thomas Hartwig, Boris Szurek, Ricardo Oliva, Casiana Vera-Cruz, Frank F White, Bing Yang, Wolf B Frommer
Plant breeders have developed crop plants that are resistant to pests, but the continual evolution of pathogens creates the need to iteratively develop new control strategies. Molecular tools have allowed us to gain deep insights into disease responses, allowing for more efficient, rational engineering of crops that are more robust or resistant to a greater number of pathogen variants. Here we describe the roles in disease progress of SWEET and STP transporters, which are membrane proteins that mediate transport of sugars across the plasma membrane...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
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