Abstract:
:Methods for installing natural and unnatural amino acids and their modifications into proteins in a benign and precise manner are highly sought-after in protein science. Here we describe a protocol for 'post-translational mutagenesis' that enables the programmed installation of protein side chains through the use of rapid, mild and operationally simple free-radical chemistry performed on recombinantly expressed and purified proteins. By introduction of protein dehydroalanine (Dha) residues (in this instance, from a unique cysteine residue introduced by site-directed mutagenesis) as free-radical trapping 'tags' for downstream modification, exquisite control over the site of subsequent modification is achieved. Using readily available alkyl halide precursors and simple borohydride salts, alkyl radicals can be generated in aqueous solution. These alkyl radicals react rapidly with protein-bound Dha residues to yield functionalized protein products with new carbon-carbon bonds. Once the Dha is installed, the introduction of the desired functionality is limited only by the requirement for polarity matching of the generated radical with the Dha 'acceptor', the solubility of the alkyl halide precursors in aqueous solution and the kinetics of the reaction itself. For example, methylated derivatives of lysine, arginine and glutamine are readily accessible. Furthermore, as the side chains are constructed chemically, many unnatural modifications can also be directly introduced as part of the side chain, including isotope reporters (19F, 13C) that can be used in biophysical experiments such as protein NMR. From a suitable cysteine mutant of the target protein, the entire procedure for this chemical post-translational mutation takes 2 d and is readily performed by nonchemists.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Wright TH,Davis BGdoi
10.1038/nprot.2017.087subject
Has Abstractpub_date
2017-10-01 00:00:00pages
2243-2250issue
10eissn
1754-2189issn
1750-2799pii
nprot.2017.087journal_volume
12pub_type
杂志文章相关文献
Nature Protocols文献大全abstract::Development of non-invasive and accurate methods to track cell fate after delivery will greatly expedite transition of embryonic stem (ES) cell therapy to the clinic. In this protocol, we describe the in vivo monitoring of stem cell survival, proliferation and migration using reporter genes. We established stable ES c...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.100
更新日期:2009-01-01 00:00:00
abstract::Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by im...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.085
更新日期:2015-11-01 00:00:00
abstract::Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.005
更新日期:2012-02-23 00:00:00
abstract::High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper the identification of rare transcripts contained within the RNA repertoire. Herein we present targeted-RNA directional sequencing (TARDIS), ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.120
更新日期:2015-12-01 00:00:00
abstract::This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.259
更新日期:2007-01-01 00:00:00
abstract::We describe the use of a microfabricated cell culture substrate, consisting of a uniform array of closely spaced, vertical, elastomeric microposts, to study the effects of substrate rigidity on cell function. Elastomeric micropost substrates are micromolded from silicon masters comprised of microposts of different hei...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.189
更新日期:2011-02-01 00:00:00
abstract::This protocol is used to produce stably transformed tobacco (Nicotiana tabacum) NT1 cell lines, using Agrobacterium tumefaciens-mediated DNA delivery of a binary vector containing a gene encoding hepatitis B surface antigen and a gene encoding the kanamycin selection marker. The NT1 cultures, at the appropriate stage ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.176
更新日期:2006-01-01 00:00:00
abstract::Chromatin and transcriptional processes are among the most intensively studied fields of biology today. The introduction of chromatin immunoprecipitations (ChIP) represents a major advancement in this area. This powerful method allows researchers to probe specific protein-DNA interactions in vivo and to estimate the d...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.27
更新日期:2006-01-01 00:00:00
abstract::Human pluripotent stem cells (hPSCs) provide a valuable model for the study of human development and a means to generate a scalable source of cells for therapeutic applications. This protocol specifies cell fate efficiently into cardiac and endothelial lineages from hPSCs. The protocol takes 2 weeks to complete and re...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.153
更新日期:2017-01-01 00:00:00
abstract::A procedure for the conversion of a symmetrical ketone to an enantiomerically pure lactam is described. The technique described here involves a ring-expansion reaction of a 4-substituted cyclohexanone accomplished with a chiral 1,3-azidopropanol derivative. The procedure entails first a one-step preparation of (R)-1-p...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.518
更新日期:2008-01-01 00:00:00
abstract::RNase H-dependent PCR-enabled T-cell receptor sequencing (rhTCRseq) can be used to determine paired alpha/beta T-cell receptor (TCR) clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples. With the enhanced specificity of RNase H-dependent PCR (rhPCR), it achieves TCR-specific...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-019-0195-x
更新日期:2019-08-01 00:00:00
abstract::Influenza A viruses (IAVs) cause epidemics and pandemics that result in considerable financial burden and loss of human life. To manage annual IAV epidemics and prepare for future pandemics, an improved understanding of how IAVs emerge, transmit, cause disease and acquire pandemic potential is urgently needed. Fundame...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.180
更新日期:2014-11-01 00:00:00
abstract::Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long read...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2018.025
更新日期:2018-06-01 00:00:00
abstract::Hypochlorous acid (HOCl) is a critical member of the reactive oxygen species (ROS) produced by immune cells to fight infections. On the other hand, HOCl in homeostasis causes oxidative damage to biomolecules and is linked to many diseases, including inflammatory, neurodegenerative, and cardiovascular diseases. Herein,...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0041-6
更新日期:2018-10-01 00:00:00
abstract::This protocol describes a culture system in which inner-ear sensory tissue is produced from mouse embryonic stem (ES) cells under chemically defined conditions. This model is amenable to basic and translational investigations into inner ear biology and regeneration. In this protocol, mouse ES cells are aggregated in 9...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.100
更新日期:2014-01-01 00:00:00
abstract::Neurotransmitter release is triggered by membrane depolarization, Ca(2+) influx and Ca(2+) sensing by the release machinery, causing synaptic vesicle (SV) fusion with the plasma membrane. Interlinked is a complex membrane cycle in which vesicles are tethered to the release site, primed, fused and recycled. As many of ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.074
更新日期:2012-06-21 00:00:00
abstract::This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli c...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.051
更新日期:2012-06-07 00:00:00
abstract::Here, we describe a robust protocol for the reverse transfection of cells on small interfering (siRNA) arrays, which, in combination with multi-channel immunofluorescence or time-lapse microscopy, is suitable for genome-wide RNA interference (RNAi) screens in intact human cells. The automatic production of 48 'transfe...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.483
更新日期:2007-01-01 00:00:00
abstract::This protocol describes the synthesis of oligo(poly(ethylene glycol) fumarate) (OPF; 1-35 kDa; a polymer useful for tissue engineering applications) by a one-pot reaction of poly(ethylene glycol) (PEG) and fumaryl chloride. The procedure involves three parts: dichloromethane and PEG are first dried; the reaction step ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.055
更新日期:2012-05-31 00:00:00
abstract::Embryonic stem cells (ESCs) constitute a tool of great potential in neurobiology, enabling the directed differentiation of specific neural cell types. We have shown recently that neurons of the cerebral cortex can be generated from mouse ESCs cultured in a chemically defined medium that contains no morphogen, but in t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.157
更新日期:2009-01-01 00:00:00
abstract::The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA dete...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.201
更新日期:2007-01-01 00:00:00
abstract::A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uch...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.085
更新日期:2012-07-19 00:00:00
abstract::Here we present a protocol for the extraction of RNA from Dictyostelium discoideum. Dictyostelium is a social amoeba that undergoes a basic developmental program, and therefore analysis of RNA levels over a time course is a commonly used technique. This procedure is similar to other guanidine thiocyanate-based methods...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.191
更新日期:2007-01-01 00:00:00
abstract::Studies on colonic cells in the lamina propria (LP) of mice are important for understanding the cellular and immune responses in the gut, especially in inflammatory bowel diseases (such as morbus crohn and colitis ulcerosa). This protocol details a method to isolate LP cells and characterize freshly isolated cells by ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.315
更新日期:2007-01-01 00:00:00
abstract::By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningf...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.164
更新日期:2014-11-01 00:00:00
abstract::Characterization of the cellular participants in tissue immune responses is crucial to understanding infection, cancer, autoimmunity, allergy, graft rejection and other immunological processes. Previous reports indicate that leukocytes in lung vasculature fail to be completely removed by perfusion. Several studies sug...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.005
更新日期:2014-01-01 00:00:00
abstract::At present, several assays that use radioisotope labeling to quantify the degradation of long-lived proteins have been developed to measure autophagic flux. Here, we describe a nonradioactive pulse-chase protocol using L-azidohomoalanine (AHA) labeling to quantify long-lived protein degradation during autophagy. AHA i...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.160
更新日期:2017-12-01 00:00:00
abstract::Electrochemically active bacteria (EAB) have the ability to transfer electrons to electron acceptors located outside the cell, and they are widely present in diverse environments. In spite of their important roles in geochemical cycles, environmental remediation and electricity generation, so far, only a limited numbe...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.173
更新日期:2014-01-01 00:00:00
abstract::The specialized microfold cells (M cells) in the follicle-associated epithelium (FAE) of intestinal Peyer's patches serve as antigen-sampling cells of the intestinal innate immune system. Unlike 'classical' enterocytes, they are able to translocate diverse particulates without digesting them. They act as pathways for ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2017.041
更新日期:2017-07-01 00:00:00
abstract::Mass spectrometry-based phosphoproteomic analysis is a powerful method for gaining a global, unbiased understanding of cellular signaling. Its accuracy and comprehensiveness stands or falls with the quality and choice of the applied phosphopeptide prefractionation strategy. This protocol covers a powerful but simple a...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.134
更新日期:2016-01-01 00:00:00