An up-to-date introduction for the uninitiated into the various "flavors" of chemical genomics with a series of readily reproducible techniques for applications in organic chemistry, protein chemistry, and computer science, emphasizing the high-throughput approaches that are the essence of chemical genomics. The techniques range from the classic design of small molecules as affinity ligands for specific protein families, to in silico docking for computational approaches to protein-small molecule interactions, to producing highly diverse collections of proteins, carbohydrates, and small molecules for use in arrays containing large numbers of these molecules. There are also methods for the production of proteins and carbohydrates using different expression systems, for analyzing proteins using mass spectrometry, and for arraying proteins and carbohydrates on solid supports. The protocols follow the successful Methods in Molecular BiologyT series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
Part I. Reviews; Introduction to Chemical Genomics; Paul R. Caron; Chemistry for Chemical Genomics; Lutz Weber; Computer-Aided Design of Small Molecules for Chemical Genomics; Philip M. Dean; Part II. Protocols; Design, Synthesis, and Screening of Biomimetic Ligands for Affinity Chromatography; Ana Cecilia A. Roque, Geeta Gupta, and Christopher R. Lowe; The Role and Application of In Silico Docking in Chemical Genomics Research; Aldo Jongejan, Chris de Graaf, Nico P. E. Vermeulen, Rob Leurs, and Iwan J. P. de Esch; Synthesis of Complex Carbohydrates and Glyconjugates: Enzymatic Synthesis of Globotetraose Using b-1, 3-N-Acetylgalactosaminyltransferase LgtD from Hemophilus Infuenzae Strain Rd; Kang Ryu, Steven Lin, Jun Shao, Jing Song, Min Chen, Wei Wang, Hanfen Li, Wen Yi, and Peng George Wang; High Throughput Cloning for Proteomics Research; Sharon A. Doyle; Screening for the Expression of Soluble Recombinant Protein in E. coli; Sharon A. Doyle; High Throughput Purification of Hexahistidine-Tagged Proteins Expressed in E. coli; Michael B. Murphy and Sharon A. Doyle; The Wheat Germ Cell-Free Expression System: Methods for High Throughput Materialization of Genetic Information; Tatsuya Sawasaki, M. D. Gouda, Takayasu Kawasaki, Takafumi Tsuboi, Yuzuru Tozawa, Kazuyuki Takai, and Yaeta Endo; Advances in Genome-Wide Protein Expression Using the Wheat Germ Cell-Free System; Yaeta Endo and Tatsuya Sawasaki; Production of Proteins for NMR Studies Using the Wheat Germ Cell-Free System; Toshiyuki Kohno; Adenoviral Expression of Reporter Proteins for High Throughput Cell-Based Screening; Jon Hoyt and Randall W. King; Fabrication of Protein Function Microarrays for Systems-Oriented Proteomic Analysis; Jonathan M. Blackburn and Darren J. Hart; Peptide and Small Molecule Microarrays; Jan Marik and Kit S. Lam; Peptide Mass Fingerprinting: Protein Identification Using MALDI-TOF Mass Spectrometry; Judith Webster and David Oxley; A Practical Protocol for Carbohydrate Microarrays; Ruobing Wang, Dhaval Shah, Shaoyi Liu, and Denong Wang; Development of a Yeast Two-Hybrid Screen for Selection of Human Ras-Raf Protein Interaction Inhibitors; Vladimir Khazak, Erica A. Golemis, and Lutz Weber