SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework for the classification of proteins.
High‐throughput Affinity Purification Mass Spectrometry (AP‐MS) experiments can identify a large number of protein interactions, but only a fraction of these interactions are biologically relevant.
The Reactome database of curated biological pathways provides a tool for visualizing user‐supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and determine whether all that are necessary ar.
pLink is a search engine for high‐throughput identification of cross‐linked peptides from their tandem mass spectra, which is the data‐analysis step in chemical cross‐linking of proteins coupled with mass spectrometry analysis.
RNA editing is a post‐transcriptional/co‐transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions.
Cultured mammalian cells are used extensively in cell biology studies. It requires a number of special skills in order to be able to preserve the structure, function, behavior, and biology of the cells in culture.
Isolated spinal motoneurons are a powerful tool for studying basic mechanisms of neurite growth and survival. Since motoneurons are a minor population of developing spinal cord cells, they need to be purified and enriched to separate them from non‐neuronal cells.
The integration of cells with their extracellular environment is facilitated by cell surface adhesion receptors, such as integrins, which play important roles in both normal development and the onset of pathologies.
The nucleus is generally found near the cell center; however its position can vary in response to extracellular or intracellular signals, leading to a polarized intracellular organization. Nuclear movement is mediated by the cytoskeleton and its associated motors.
One concept in regenerative therapy is the replacement of a lost or damaged organ with a regenerated, fully functional organ.
The complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction‐unlimited fluorescence microscopy to resolve them.
Purification of single‐chirality single‐wall carbon nanotubes (SWCNTs) from their synthetic mixture is a prerequisite for many applications.
Rapid and reversible methods for altering the function of endogenous proteins are not only indispensable tools for probing complex biological systems, but may potentially drive the development of new therapeutics for the treatment of human diseases.
This article describes methods for a new, non‐antibody phosphorylation detection reagent, termed pIMAGO (phospho‐imaging).
This article presents a detailed description of intraperitoneal and oral glucose tolerance tests in mice. The former is widely used in initial high‐throughput phenotyping of mutant mice to assess a diabetic phenotype and alterations in glucose homeostasis.
Mass spectrometry–based quantitative proteomics is a powerful method for in‐depth exploration of protein expression, allowing researchers to probe its regulation and study signal‐transduction networks, protein turnover, secretion, and spatial distribution, as well as post‐translational modi.
Three commonly used murine surgical models of bone healing [closed fracture with intramedullary fixation, distraction osteogenesis (DO), and marrow ablation by reaming] are presented. Detailed surgical protocols for each model are outlined.
Fractures are one of the most common large‐organ, traumatic injuries in humans, and osteoporosis‐related fractures are the fastest growing health care problem of aging.
Providing anesthesia and analgesia for mouse subjects is a common and critical practice in the laboratory setting.
An efficient, reliable method for the chemical synthesis of (E)‐5‐[3‐aminoallyl]‐uridine‐5′‐O‐triphosphate (AA‐UTP), starting from 5‐iodouridine, is described.
Microwave‐assisted chemical phosphitylation of novel nucleoside analogs containing a ribulose sugar unit was successful with yields ranging from 50% to 79% using 2‐cyanoethyl‐N,N‐diisopropyl chlorophosphoramidite as the phosphitylating reagent.
This unit contains a complete procedure for the detection and structural characterization of DNA protein crosslinks (DPCs). The procedure also describes an approach for the quantitation of the various structurally distinct DPCs.
This unit describes the synthesis of γ‐phosphate‐labeled and doubly labeled adenosine triphosphate (ATP) analogs and their characterization using the phosphodiesterase I from Crotalus adamanteus (snake venom phosphodiesterase; SVPD).
The use of pronucleotides to circumvent the well‐known drawbacks of nucleotide analogs has played a significant role in the area of antiviral and anticancer drug delivery.
Only one out of four mammalian arrestin subtypes, arrestin‐3, facilitates the activation of JNK family kinases. Here we describe two different protocols used for elucidating the mechanisms involved.
Highlighted in this unit are issues that should be considered when recording glutamate receptors at the single‐channel level, including some commonly encountered problems and their remedies. “UNIT 11.
This is a companion to UNIT 11.16: Single‐Channel Recording of Glutamate Receptors. Described here are techniques for analyzing single‐channel currents recorded from glutamate receptors to characterize their properties.
The establishment of reproducible mouse models of acute lymphoblastic leukemia (ALL) is necessary to provide in vivo therapeutic test systems that recapitulate human ALL, and for amplification of limited amounts of primary tumor material.