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https://www.readbyqxmd.com/read/28191579/synthetic-mimics-of-biotin-strept-avidin
#1
Wenqi Liu, Soumen K Samanta, Bradley D Smith, Lyle Isaacs
Biotin/(strept)avidin self-assembly is a powerful platform for nanoscale fabrication and capture with many different applications in science, medicine, and nanotechnology. However, biotin/(strept)avidin self-assembly has several well-recognized drawbacks that limit performance in certain technical areas and there is a need for synthetic mimics that can either become superior replacements or operational partners with bio-orthogonal recognition properties. The goal of this tutorial review is to describe the recent progress in making high affinity synthetic association partners that operate in water or biological media...
February 13, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28151642/tyrosine-selective-functionalization-for-bio-orthogonal-cross-linking-of-engineered-protein-hydrogels
#2
Christopher M Madl, Sarah C Heilshorn
Engineered protein hydrogels have shown promise as artificial extracellular matrix materials for the 3D culture of stem cells due to the ability to decouple hydrogel biochemistry and mechanics. The modular design of these proteins allows for incorporation of various bioactive sequences to regulate cellular behavior. However, the chemistry used to cross-link the proteins into hydrogels can limit what bioactive sequences can be incorporated, in order to prevent nonspecific cross-linking within the bioactive region...
February 2, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28107619/peptide-based-stealth-nanoparticles-for-targeted-and-ph-triggered-delivery
#3
Alessandro Ranalli, Melissa Santi, Luigi Capriotti, Valerio Voliani, David Porciani, Fabio Beltram, Giovanni Signore
Stealth agents are extensively investigated as a means by which to prolong nanostructure residence time in the bloodstream by avoiding uptake by the reticuloendothelial system. Unfortunately, commonly used agents such as poly(ethylene glycol) can adversely impact targeting efficiency and promote immune reaction by the host organism. Therefore, there is an increasing interest in developing biocompatible, non-PEGylated organic nanostructures able to perform targeted delivery to increase the efficacy of liposomal technology...
February 3, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28074971/bio-orthogonal-click-and-release-donation-of-caged-carbonyl-sulfide-cos-and-hydrogen-sulfide-h2s
#4
Andrea K Steiger, Yang Yang, Maksim Royzen, Michael D Pluth
Hydrogen sulfide (H2S) is an important biomolecule with high therapeutic potential. Here we leverage the inverse-electron demand Diels-Alder (IEDDA) click reaction between a thiocarbamate-functionalized trans-cyclooctene and a tetrazine to deliver carbonyl sulfide (COS), which is quickly converted to H2S by the uniquitous enzyme carbonic anhydrase (CA), thus providing a new strategy for bio-orthogonal COS/H2S donation.
January 11, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28058282/protein-degradation-by-in-cell-self-assembly-of-proteolysis-targeting-chimeras
#5
Honorine Lebraud, David J Wright, Christopher N Johnson, Tom D Heightman
Selective degradation of proteins by proteolysis targeting chimeras (PROTACs) offers a promising potential alternative to protein inhibition for therapeutic intervention. Current PROTAC molecules incorporate a ligand for the target protein, a linker, and an E3 ubiquitin ligase recruiting group, which bring together target protein and ubiquitinating machinery. Such hetero-bifunctional molecules require significant linker optimization and possess high molecular weight, which can limit cellular permeation, solubility, and other drug-like properties...
December 28, 2016: ACS Central Science
https://www.readbyqxmd.com/read/28028885/antibiotic-spider-silk-site-specific-functionalization-of-recombinant-spider-silk-using-click-chemistry
#6
David Harvey, Philip Bardelang, Sara L Goodacre, Alan Cockayne, Neil R Thomas
In a new, versatile approach to fun-ction-alizing recombinant spider silk, L-azidohomoalanine is introduced residue-specifically in the minispidroin protein 4RepCT through expression in an E. coli methionine auxotroph. Both fluorophores and the antibiotic levofloxacin are attached to this bio-orthogonal amino acid using copper-catalyzed click chemistry, either before or after the silk fibers are self-assembled.
December 28, 2016: Advanced Materials
https://www.readbyqxmd.com/read/28008983/scaffold-free-bio-orthogonal-assembly-of-3-dimensional-cardiac-tissue-via-cell-surface-engineering
#7
Dmitry Rogozhnikov, Paul J O'Brien, Sina Elahipanah, Muhammad N Yousaf
There has been tremendous interest in constructing in vitro cardiac tissue for a range of fundamental studies of cardiac development and disease and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress towards studying 2-dimensional cardiac function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free 3-dimensional multiple cell type co-culture cardiac tissue models. Herein, we develop a programmed rapid self-assembly strategy to induce specific and stable cell-cell contacts among multiple cell types found in heart tissue to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes...
December 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28000660/a-crotonyl-coa-reductase-carboxylase-independent-pathway-for-assembly-of-unusual-alkylmalonyl-coa-polyketide-synthase-extender-units
#8
Lauren Ray, Timothy R Valentic, Takeshi Miyazawa, David M Withall, Lijiang Song, Jacob C Milligan, Hiroyuki Osada, Shunji Takahashi, Shiou-Chuan Tsai, Gregory L Challis
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters...
December 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27941914/high-fidelity-visualization-of-cell-to-cell-variation-and-temporal-dynamics-in-nascent-extracellular-matrix-formation
#9
Claire M McLeod, Robert L Mauck
Extracellular matrix dynamics are key to tissue morphogenesis, homeostasis, injury, and repair. The spatiotemporal organization of this matrix has profound biological implications, but is challenging to monitor using standard techniques. Here, we address these challenges by using noncanonical amino acid tagging to fluorescently label extracellular matrix synthesized in the presence of bio-orthogonal methionine analogs. This strategy labels matrix proteins with high resolution, without compromising their distribution or mechanical function...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27925692/a-method-to-generate-and-analyze-modified-myristoylated-proteins
#10
Huanyao Gao, Wei Sun, Zhiquan Song, Yanbao Yu, Li Wang, Xian Chen, Qisheng Zhang
Covalent lipid modification of proteins is essential to their cellular localizations and functions. Engineered lipid motifs, coupled with bio-orthogonal chemistry, have been utilized to identify myristoylated or palmitoylated proteins in cells. However, whether modified proteins have similar properties as endogenous ones has not been well investigated mainly due to lack of methods to generate and analyze purified proteins. We have developed a method that utilizes metabolic interference and mass spectrometry to produce and analyze modified, myristoylated small GTPase ADP-ribosylation factor 1 (Arf1)...
February 1, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27812569/catalytic-promiscuity-of-glycopeptide-n-methyltransferases-enables-bio-orthogonal-labelling-of-biosynthetic-intermediates
#11
Clara Brieke, Grace Yim, Madeleine Peschke, Gerard D Wright, Max J Cryle
We show that two α-N-methyltransferases involved in the biosynthesis of glycopeptide antibiotics (GPAs) already recognise partly crosslinked precursor peptides of teicoplanin aglycone indicating that in vivo N-methylation can occur as an early tailoring step during GPA biosynthesis. This relaxed substrate specificity is accompanied by a remarkable promiscuity regarding the co-substrate enabling modulation of biological activity and the introduction of reactive handles which could be further modified using bio-orthogonal chemistry...
November 17, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27775236/half-life-extension-of-biopharmaceuticals-using-chemical-methods-alternatives-to-pegylation
#12
REVIEW
Søren B van Witteloostuijn, Søren L Pedersen, Knud J Jensen
Peptides and proteins constitute a vast pool of excellent drug candidates. Evolution has equipped these molecules with superior drug-like properties such as high specificity and potency. However, native peptides and proteins suffer from an inadequate pharmacokinetic profile, and their outstanding pharmacological potential can only be realized if this issue is addressed during drug development. To overcome this challenge, a variety of half-life extension techniques relying on covalent chemical modification have been developed...
November 21, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27764671/nascent-proteome-remodeling-following-homeostatic-scaling-at-hippocampal-synapses
#13
Christoph T Schanzenbächer, Sivakumar Sambandan, Julian D Langer, Erin M Schuman
Homeostatic scaling adjusts the strength of synaptic connections up or down in response to large changes in input. To identify the landscape of proteomic changes that contribute to opposing forms of homeostatic plasticity, we examined the plasticity-induced changes in the newly synthesized proteome. Cultured rat hippocampal neurons underwent homeostatic up-scaling or down-scaling. We used BONCAT (bio-orthogonal non-canonical amino acid tagging) to metabolically label, capture, and identify newly synthesized proteins, detecting and analyzing 5,940 newly synthesized proteins using mass spectrometry and label-free quantitation...
October 19, 2016: Neuron
https://www.readbyqxmd.com/read/27724898/direct-imaging-of-glycans-in-arabidopsis-roots-via-click-labeling-of-metabolically-incorporated-azido-monosaccharides
#14
Jorin Hoogenboom, Nathalja Berghuis, Dario Cramer, Rene Geurts, Han Zuilhof, Tom Wennekes
BACKGROUND: Carbohydrates, also called glycans, play a crucial but not fully understood role in plant health and development. The non-template driven formation of glycans makes it impossible to image them in vivo with genetically encoded fluorescent tags and related molecular biology approaches. A solution to this problem is the use of tailor-made glycan analogs that are metabolically incorporated by the plant into its glycans. These metabolically incorporated probes can be visualized, but techniques documented so far use toxic copper-catalyzed labeling...
October 10, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27723242/p-azidophenylarsenoxide-an-arsenical-bait-for-the-in-situ-capture-and-identification-of-cellular-arsenic-binding-proteins
#15
Xiaowen Yan, Jinhua Li, Qingqing Liu, Hanyong Peng, Aleksandra Popowich, Zhixin Wang, Xing-Fang Li, X Chris Le
Identification of arsenic-binding proteins is important for understanding arsenic health effects and for developing arsenic-based therapeutics. We report here a strategy for the capture and identification of arsenic-binding proteins in living cells. We designed an azide-labeled arsenical, p-azidophenylarsenoxide (PAzPAO), to serve bio-orthogonal functions: the trivalent arsenical group binds to cellular proteins in situ, and the azide group facilitates click chemistry with dibenzylcyclooctyne. The selective and efficient capture of arsenic-binding proteins enables subsequent enrichment and identification by shotgun proteomics...
October 10, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27721014/genetically-encoding-new-bioreactivity
#16
Lei Wang
The genetic code can be expanded to include unnatural amino acids (Uaas) by engineering orthogonal components involved in protein translation. To be compatible with live cells, side chains of Uaas have been limited to either chemically inert or bio-orthogonal (i.e., nonreactive toward biomolecules) functionalities. To introduce bioreactivity into live systems, the genetic code has recently been engineered to encode a new class of Uaas, the bioreactive Uaas. These Uaas, after being incorporated into proteins, specifically react with target natural amino acid residues via proximity-enabled bioreactivity, enabling the selective formation of new covalent linkages within and between proteins both in vitro and in live systems...
October 6, 2016: New Biotechnology
https://www.readbyqxmd.com/read/27708265/spatiotemporal-control-of-cell-cell-reversible-interactions-using-molecular-engineering
#17
Peng Shi, Enguo Ju, Zhengqing Yan, Nan Gao, Jiasi Wang, Jianwen Hou, Yan Zhang, Jinsong Ren, Xiaogang Qu
Manipulation of cell-cell interactions has potential applications in basic research and cell-based therapy. Herein, using a combination of metabolic glycan labelling and bio-orthogonal click reaction, we engineer cell membranes with β-cyclodextrin and subsequently manipulate cell behaviours via photo-responsive host-guest recognition. With this methodology, we demonstrate reversible manipulation of cell assembly and disassembly. The method enables light-controllable reversible assembly of cell-cell adhesion, in contrast with previously reported irreversible effects, in which altered structure could not be reused...
October 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27693784/non-invasive-stem-cell-tracking-in-hindlimb-ischemia-animal-model-using-bio-orthogonal-copper-free-click-chemistry
#18
Si Yeon Lee, Sangmin Lee, Jangwook Lee, Ji Young Yhee, Hwa In Yoon, Soon-Jung Park, Heebeom Koo, Sung-Hwan Moon, Hyukjin Lee, Yong Woo Cho, Sun Woong Kang, Sang-Yup Lee, Kwangmeyung Kim
Labeling of stem cells aims to distinguish transplanted cells from host cells, understand in vivo fate of transplanted cells, particularly important in stem cell therapy. Adipose-derived mesenchymal stem cells (ASCs) are considered as an emerging therapeutic option for tissue regeneration, but much remains to be understood regarding the in vivo evidence. In this study, a simple and efficient cell labeling method for labeling and tracking of stem cells was developed based on bio-orthogonal copper-free click chemistry, and it was applied in a mouse hindlimb ischemia model...
October 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27642274/bio-orthogonally-crosslinked-engineered-protein-hydrogels-with-tunable-mechanics-and-biochemistry-for-cell-encapsulation
#19
Christopher M Madl, Lily M Katz, Sarah C Heilshorn
Covalently-crosslinked hydrogels are commonly used as 3D matrices for cell culture and transplantation. However, the crosslinking chemistries used to prepare these gels generally cross-react with functional groups present on the cell surface, potentially leading to cytotoxicity and other undesired effects. Bio-orthogonal chemistries have been developed that do not react with biologically relevant functional groups, thereby preventing these undesirable side reactions. However, previously developed biomaterials using these chemistries still possess less than ideal properties for cell encapsulation, such as slow gelation kinetics and limited tuning of matrix mechanics and biochemistry...
June 7, 2016: Advanced Functional Materials
https://www.readbyqxmd.com/read/27605302/site-specific-fluorescent-labeling-to-visualize-membrane-translocation-of-a-myristoyl-switch-protein
#20
Sung-Tae Yang, Sung In Lim, Volker Kiessling, Inchan Kwon, Lukas K Tamm
Fluorescence approaches have been widely used for elucidating the dynamics of protein-membrane interactions in cells and model systems. However, non-specific multi-site fluorescent labeling often results in a loss of native structure and function, and single cysteine labeling is not feasible when native cysteines are required to support a protein's folding or catalytic activity. Here, we develop a method using genetic incorporation of non-natural amino acids and bio-orthogonal chemistry to site-specifically label with a single fluorescent small molecule or protein the myristoyl-switch protein recoverin, which is involved in rhodopsin-mediated signaling in mammalian visual sensory neurons...
September 8, 2016: Scientific Reports
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