Chemical Proteomics: Methods and Protocols by Marcus Bantscheff (auth.), Gerard Drewes, Marcus Bantscheff

By Marcus Bantscheff (auth.), Gerard Drewes, Marcus Bantscheff (eds.)

The multidisciplinary technological know-how of chemical proteomics reports how small molecules of artificial or ordinary starting place bind to proteins and modulate their functionality. In Chemical Proteomics: tools and Protocols, specialist researchers within the box offer key suggestions to enquire chemical proteomics concentrating on analytical options, how probes are generated, ideas for the invention of small molecule ambitions and the probing of objective functionality, and small molecule ligand and drug discovery. Written within the hugely winning Methods in Molecular Biology™ sequence structure, chapters contain introductions to their respective themes, lists of the required fabrics and reagents, step by step, with ease reproducible laboratory protocols, and key tips about troubleshooting and warding off recognized pitfalls.

Authoritative and sensible, Chemical Proteomics : tools and Protocols seeks to supply methodologies that would give a contribution to a much broader software of chemical proteomics equipment in biochemical and mobile organic laboratories.

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4. 2% AgNO3, for 20 min. 5. Discard the silver nitrate in heavy metal waste and wash the gel again (three times for 20 s). Transfer the gel into a clean Petri dish after the second wash step to keep the background as low as possible. 6. 05% formaldehyde. Rock the Petri dish until the solution changes to a yellow color. Remove the liquid and allow the development without liquid. If the staining is not sufficient, repeat the developing step. 7. When all the bands are visible on the gel, quench the developer by removing the liquid from the Petri dish and adding 5% acetic acid.

2. Agitate the solution on an orbital shaker for 45 min in the dark at room temperature. 3. After 45 min, add the modified FLAG® peptide to the mixture to a final concentration of 1 mM (see Note 3). 4. Continue to agitate the solution for another 45 min on the orbital shaker. 5. In the meantime, prepare 4 mL of a Sephadex G-25 slurry in water, using a Sephadex to water ratio of 75:25. Carefully pour the slurry into a 3–5 mL plastic column. Wash the resin in the column with two column volumes of water.

Notably, SMPCs offer several advantages compared to biotinylated probes. , the peptide) in SMPCs can be kept to a minimum to preserve the biological activity of the probe, in contrast to the extended linkers required for biotinylated probes to dock into the deep binding pocket on avidin. Moreover, by carefully choosing the amino acid composition of the peptide, the hydrophilic properties of the SMPC can be controlled to mimic the behavior of the probe molecule. Conceptually, the design of SMPCs follows the basic design principles of typical fishing probes, which are widely utilized in chemoproteomics experiments.

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