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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 motif coupled with bio-orthogonal chemistry has 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)...
December 7, 2016: Chembiochem: a European Journal of Chemical Biology
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
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
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
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
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
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
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
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
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
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
Xinxin Gao, Rami N Hannoush
Wnt palmitoylation regulates its secretion and signaling activity in cells. Methods to monitor cellular Wnt palmitoylation are instrumental in investigating Wnt activity, secretion, and its interaction with cellular membrane compartments. This protocol describes a method we have recently developed to detect cellular Wnt palmitoylation. The method, combining click chemistry, bio-orthogonal fatty acid probes, and proximity ligation assay (PLA), provides high sensitivity and subcellular resolution for detection of Wnt palmitoylation...
2016: Methods in Molecular Biology
Sarah Calve, Andrew J Witten, Alexander R Ocken, Tamara L Kinzer-Ursem
Analysis of the developing proteome has been complicated by a lack of tools that can be easily employed to label and identify newly synthesized proteins within complex biological mixtures. Here, we demonstrate that the methionine analogs azidohomoalanine and homopropargylglycine can be globally incorporated into the proteome of mice through facile intraperitoneal injections. These analogs contain bio-orthogonal chemical handles to which fluorescent tags can be conjugated to identify newly synthesized proteins...
2016: Scientific Reports
Romain Aufaure, Julie Hardouin, Nadine Millot, Laurence Motte, Yoann Lalatonne, Erwann Guénin
Inverse electron demand Diels-Alder (iEDDA) was evaluated for the functionalization of gold nanoparticles. The reaction was first modelled with the free coating molecule 1-hydroxy-1,1-methylenebisphosphonate bearing an alkene functionality (HMBPene). A model tetrazine 3,6-dipyridin-2-yl-1,2,4,5-tetrazine (pyTz) was used, kinetic of the reaction was calculated and coupling products were analysed by NMR and HRMS. The reaction was then transposed at the nanoparticle surface. Gold nanoparticles bearing an alkene functionality were obtained using a one-pot methodology with HMBPene and the tetrazine click chemistry was evaluated at their surface using pyTz...
November 2, 2016: Chemistry: a European Journal
Sarah M Wells, John C Widen, Daniel A Harki, Kay M Brummond
The Nicholas reaction has been applied to the installation of alkyne ligation handles. Acid-promoted propargylation of hydroxyl, sulfhydryl, amino, and carboxyl groups using dicobalt hexacarbonyl-stabilized propargylium ions is reported. This method is useful for introduction of propargyl groups into base-sensitive molecules, thereby expanding the toolbox of methods for the incorporation of alkynes for bio-orthogonal reactions. High-value molecules are used as the limiting reagent, and various propargylium ion precursors are compared...
September 16, 2016: Organic Letters
Dmitry Rogozhnikov, Wei Luo, Sina Elahipanah, Paul J O'Brien, Muhammad N Yousaf
There has been tremendous interest in constructing in vitro liver organ models for a range of fundamental studies of cell signaling, metabolism, and infectious diseases, and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress toward studying two-dimensional hepatic function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free three-dimensional multiple cell line coculture tissue models of liver. Herein, we develop and employ a strategy to induce specific and stable cell-cell contacts among multiple hepatic cell lines to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes...
September 21, 2016: Bioconjugate Chemistry
Jigang Wang, Jianbin Zhang, Yew-Mun Lee, Pin-Lang Koh, Shukie Ng, Feichao Bao, Qingsong Lin, Han-Ming Shen
Autophagy is an intracellular degradation mechanism in response to nutrient starvation. Via autophagy, some nonessential cellular constituents are degraded in a lysosome-dependent manner to generate biomolecules that can be utilized for maintaining the metabolic homeostasis. Although it is known that under starvation the global protein synthesis is significantly reduced mainly due to suppression of MTOR (mechanistic target of rapamycin serine/threonine kinase), emerging evidence demonstrates that de novo protein synthesis is involved in the autophagic process...
October 2, 2016: Autophagy
Claudia Schmidt-Dannert, Fernando Lopez-Gallego
Advances in biological engineering and systems biology have provided new approaches and tools for the industrialization of biology. In the next decade, advanced biocatalytic systems will increasingly be used for the production of chemicals that cannot be made by current processes and/or where the use of enzyme catalysts is more resource efficient with a much reduced environmental impact. We expect that in the future, manufacture of chemicals and materials will utilize both biocatalytic and chemical synthesis synergistically...
September 2016: Microbial Biotechnology
Loai K E A Abdelmohsen, David S Williams, Jan Pille, Sema G Ozel, Roger S M Rikken, Daniela A Wilson, Jan C M van Hest
Polymersomes are robust, versatile nanostructures that can be tailored by varying the chemical structure of copolymeric building blocks, giving control over their size, shape, surface chemistry, and membrane permeability. In particular, the generation of nonspherical nanostructures has attracted much attention recently, as it has been demonstrated that shape affects function in a biomedical context. Until now, nonspherical polymersomes have only been constructed from nondegradable building blocks, hampering a detailed investigation of shape effects in nanomedicine for this category of nanostructures...
August 3, 2016: Journal of the American Chemical Society
Emily N Pierce, Sujeewa C Piyankarage, Tareisha Dunlap, Vladislav Litosh, Marton I Siklos, Yue-Ting Wang, Gregory R J Thatcher
Electrophilic reactive intermediates resulting from drug metabolism have been associated with toxicity and off-target effects and in some drug discovery programs trigger NO-GO decisions. Many botanicals and dietary supplements are replete with such reactive electrophiles, notably Michael acceptors, which have been demonstrated to elicit chemopreventive mechanisms; and Michael acceptors are gaining regulatory approval as contemporary cancer therapeutics. Identifying protein targets of these electrophiles is central to understanding potential therapeutic benefit and toxicity risk...
July 18, 2016: Chemical Research in Toxicology
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