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Conformational changes in protein complexes induced by ligand-drug binding, oligomerization or post-translational modifications can be determined using LC-MS/MS after cross-linking with bis(sulfosuccinimidyl)suberate.
ChIP analysis of woody plant tissue has been largely unsuccessful. Here, the Chiang lab provides their validated ChIP protocol that has been highly optimized for the analysis of wood-forming tissues.
The natural state of DNA is to be supercoiled, and therefore it is relevant use this form in studying its interactions. This protocol describes how to probe the dynamics of individual naturally supercoiled circular DNA plasmids tethered between a polystyrene bead and a glass slide.
This protocol describes procedures for the preparation and characterization of microcrystals for serial femtosecond crystallography in lipidic cubic phase (LCP-SFX) for protein structure determination at X-ray free-electron lasers (XFELs).
Lewy bodies and Lewy neurites are found in the brains of patients with Parkinson's disease and other synucleinopathies. This protocol describes how to model this by inducing α-synuclein aggregates in a primary neuronal culture system.
The authors of this protocol describe a similarity-based, large-scale approach to predicting novel drug-drug interactions (DDIs) integrating a reference standard database of known DDIs with drug similarity information from a variety of sources.
This protocol describes how to engineer and transplant either a natural decellularized donor trachea or an artificial electrospun nanofiber scaffold into a rat, providing a model for tracheal transplantation that has been successfully used in humans.
In this Protocol, the authors describe a DNA assembly method that enables users to achieve the ordered, recombination-based assembly of repetitive sequences for the development and optimization of metabolic pathways and functional genetic circuits.
In this protocol the authors describe a biochemical approach to identify ligand-receptor interactions in discovery mode with extracellular domain IgG fusion baits, tissue-extracted preys, and shotgun proteomic analysis.
Interaction between a drug and its protein target results in a shift in thermal stability of that protein. The cellular thermal shift assay–CETSA–exploits this to characterize intracellular drug-protein engagement.
Kustatscher et al. describe ChEP, an improvement on the classic chromatin pellet method that enables users to take a 'snapshot' of chromatin, making possible the isolation and identification of the full range of chromatin-binding proteins.
This protocol describes an optimized cell fractionation protocol for obtaining nuclei (or soluble and insoluble nuclear fractions) uncontaminated by cytoplasm or organelles— critical for studying nuclear RNAi or other nucleus-specific processes.
A quick route towards new radiofluorinated tracers is important for the development of PET imaging. An efficient, reliable method for optimizing radiofluorination conditions using a microfluidic chemistry approach is described in this protocol.
When a nanoparticle enters the bloodstream, proteins bind to it to form a corona that may affect its function. This protein corona can be investigated using gel electrophoresis and LC-MS.
Intrinsically disordered proteins are structurally highly flexible. This protocol describes the steps and NMR setup for performing in-cell NMR of such proteins, using human α-synuclein overexpressed in Escherichia coli as an example.
Methylglyoxal accumulates as a result of tissue damage in aging and disease. This quantitative analytical LC-MS/MS procedure can be performed on blood plasma, cultured cells, and plant and animal tissues.
This approach uses fluorescently labeled aptamers and graphene oxide nanosheets to adsorb the aptamers and quench fluorescence. Ligand (e.g., ATP or GTP) binding results in the release of aptamers into solution and fluorescence is "turned on".
Sesquiterpenes are plant-derived secondary metabolites with applications in medicine and nutrition. This protocol focuses on the metabolite analysis required to inform iterative genetic modification of Saccharomyces cerevisiae strains designed to produce a specific sesquiterpene.
Crispr/Cas technology is a quick and efficient method of modifying the genomes of a range of organisms. Here the Jaenisch laboratory provides a protocol for CRISPR/Cas-mediated genome modification of mice.
