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This protocol describes the FTMap family of web servers for determining and characterizing ligand-binding hot spots of macromolecules, including FTSite for predicting ligand-binding sites, FTFlex for accounting for side chain flexibility, FTMap/param for parameterizing additional probes, and FTDyn for mapping ensembles of protein structures.
Thanks to advances in MS/MS acquisition rates and improvements in sample preparation and HPLC separation, it is now possible to analyze the yeast proteome in a single 70-min LC-MS/MS run.
This protocol uses RNAi-based biosynthetic pathway screens combined with genetic and biochemical analyses to identify the functions of non-nucleic acid-based metabolites such as lipids beyond their roles in metabolism.
The protocol by Guo et al. for single-cell reduced-representation bisulfite sequencing (scRRBS) enables methylation profiling of individual genomes. Single-cell methods help elucidate levels of variation between individual cells within a group.
This protocol uses fluorescence recovery after photobleaching (FRAP) to dissect the reaction dynamics leading to protein turnover in macromolecular complexes in living cells.
4sUDRB-seq is a genome-wide method for measuring the transcription rate of actively transcribed genes. It can provide information on the speed of elongation and on the rate at which RNA polymerase II makes the transition into active elongation.
Cheow et al. provide a protocol for SCRAM, a method for determining DNA methylation status at defined target sites in single cells. It is reliable, low in cost and relatively fast, making it a good option when full genome coverage is not required.
Carrier mobility is the most important parameter for assessing charge carrier transfer. This protocol describes a tool for predicting the charge carrier mobilities of π-stacked systems such as organic semiconductors and the DNA double helix.
Through screening libraries of polymer nanoparticles (NPs) containing various comonomers, it is possible to develop NPs with high affinity for target biomacromolecules. This protocol describes the preparation and characterization of melittin-binding NPs.
This protocol describes an efficient double-click reaction between dialkynyl linkers and diazido peptides for generating peptides that are stabilized in an α-helical conformation. The method enables modular control over the staple linkage itself.
This protocol describes live imaging of axonal transport in Drosophila pupal brains. It complements previous techniques for imaging larval neurons by enabling the study of extensive changes occurring during metamorphosis.
Hydrogenation of functionalized substrates often relies on expensive noble metal—based catalysts. Jagadeesh et al. detail the hydrogenation of nitroarenes and the reductive amination of aldehydes with nitroarenes performed with an iron-based catalyst.
Optically active, chiral quantum dots can be prepared using chiral ligands. These nanoparticles have potential applications in photocatalysis and biological imaging, as well as in assays and sensors in asymmetric synthesis and enantioseparation.
In this model, the middle cerebral artery (MCA) is occluded with a fibrin-rich allogeneic clot, producing an embolic model of MCA occlusion in the rat that mimics the key components of neurovascular damage observed in human ischemic stroke.
This protocol describes mouse and rat models of Roux-en-Y gastric bypass and sleeve gastrectomy, which are similar to bariatric operations performed to treat obese humans.
There is a growing demand for renewable transportation fuels. This protocol describesthe production of an acetone-butanol-ethanol mixture in Clostridiumacetobutylicum as well as its reaction to form long-chain ketones for testing as car or jet fuel.
Sortase A can be used for the site-specific modification of proteins. This protocol describes its immobilization on Sepharose beads, allowing for larger-scale continuous flow reactions or easy separation from the enzyme in batch reactions.
This protocol enables the statistical analysis of cell motility in 2D and 3D microenvironments using the anisotropic persistent random walk model, providing a new tool to characterize 3D cell migration.
This protocol describes how to prepare a sequencing library for MethylC-seq analysis, enabling the methylation status of cytosines in genomic DNA to be determined at nucleotide resolution on a genome-wide scale.
With this protocol rat livers can be kept viable for up to 96 h and transplanted successfully. The livers are first loaded with cryoprotectants to prevent ice formation and protect against hypothermic injury, and they are then cooled to –6 °C without freezing.