The multidisciplinary science of chemical proteomics studies how small molecules of synthetic or natural origin bind to proteins and modulate their function. In "Chemical Proteomics: Methods and Protocols", expert researchers in the field provide key techniques to investigate chemical proteomics focusing on analytical strategies, how probes are generated, techniques for the discovery of small molecule targets and the probing of target function, and small molecule ligand and drug discovery.
Written in the highly successful Methods in "Molecular Biology" series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, "Chemical Proteomics: Methods and Protocols" seeks to provide methodologies that will contribute to a wider application of chemical proteomics methods in biochemical and cell biological laboratories.
Part I: Introduction
1 Mass Spectrometry-Based Chemoproteomic Approaches
2. Chemical Proteomics in Drug Discovery
Part II: Small Molecules and Probe Design
3. Compound Immobilization and Drug-Affinity Chromatography
4. Affinity-based Chemoproteomics with Small Molecule-Peptide Conjugates
5. A Chemical Proteomic Probe for Detecting Dehydrogenases: Catechol Rhodanine
6. Probing Proteomes with Benzophenone Photoprobes
7. Biotinylated Probes for the Analysis of Protein Modification by Electrophiles
8. Profiling of Methyltransferases and Other S-adenosyl-l-homocysteine-Binding Proteins by Capture Compound Mass Spectrometry (CCMS)
Part III: Target Discovery and Target Validation
9. Identifying Cellular Targets of Small-Molecule Probes and Drugs with Biochemical Enrichment and SILAC
10. Determination of Kinase Inhibitor Potencies in Cell Extracts by Competition Binding Assays and Isobaric Mass Tags
11. Affinity-Based Profiling of Dehydrogenase Subproteomes
12. Probing the Specificity of Protein-Protein Interactions by Quantitative Chemical Proteomics
13. Fluorescence-Based Proteasome Activity Profiling
14. Chemical Cross-Linking and High-Resolution Mass Spectrometry to Study Protein-Drug Interactions
15. Monitoring Ligand Modulation of Protein-Protein Interactions by Chemical Cross-Linking and High-Mass MALDI Mass Spectrometry
16. Time-Controlled Transcardiac Perfusion Crosslinking for In Vivo Interactome Studies
Part IV: Ligand Discovery
17. Ligand Discovery Using Small-Molecule Microarrays
18. Working with Small Molecules - Preparing and Storing Stock Solutions and Determination of Kinetic Solubility
19. A Database for Chemical Proteomics - ChEBI
20. Working with Small Molecules: Rules-of-Thumb of "Drug Likeness"
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