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 experiences how small molecules of artificial or common starting place bind to proteins and modulate their functionality. In Chemical Proteomics: tools and Protocols, specialist researchers within the box offer key ideas to enquire chemical proteomics targeting analytical concepts, how probes are generated, recommendations for the invention of small molecule pursuits and the probing of aim 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 mandatory fabrics and reagents, step by step, effectively reproducible laboratory protocols, and key pointers on troubleshooting and averting identified pitfalls.

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

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1. 1. Preparation of the Modified FLAG®-Coupled Bisindolylmaleimide-III (SMPC for Capturing of Protein Targets from Cell Lysates) 1. 6 M phosphate buffer (see Note 2). The reaction scheme is shown in Fig. 1. 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.

Chemical Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 1007/978-1-61779-364-6_4, © Springer Science+Business Media, LLC 2012 39 40 C. Saxena complicates the characterization of their affinity toward the protein targets after immobilization. Frequently, immobilized molecules on solid support exhibit lower affinities for their target proteins compared to their free state. This could lead to unacceptable losses of target proteins during the washing steps. Circumventing some of these limitations, small molecule-peptide conjugates (SMPCs) provide an orthogonal strategy to capture the targets of small molecules from biological lysates (3).

When the lysates are run through the gel it can be transferred to the nitrocellulose membrane or used for silver staining. 7. Silver Staining This section is illustrated in Fig 3a. 1. Perform all the following steps in a dust-free cabinet to minimize keratin contamination. First, fix the gel with 40% ethanol and 10% acetic acid (always add sufficient solution to completely cover the gel) for 1 h at room temperature on a rocker or at 4°C overnight. 2. Wash the gel two times with 30% ethanol for 20 min and for another 20 min with water (pro analysi).

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