Chemical Genomics

by Zanders, Edward D., PH.D.

• ISBN13: 9781588293992
• ISBN10: 1588293998
• Format: Hardcover
• Copyright: 2005-08-01
• Publisher: Humana Pr Inc

Summary

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 Biology'„¢ 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.

Table of Contents

Preface	v
Contributors	ix
PART I REVIEWS
1 Introduction to Chemical Genomics
Paul R. Caron	3	(8)
2 Chemistry for Chemical Genomics
Lutz Weber	11	(14)
3 Computer-Aided Design of Small Molecules for Chemical Genomics
Philip M. Dean	25	(18)
PART II PROTOCOLS
4 Design, Synthesis, and Screening of Biomimetic Ligands for Affinity Chromatography
Ana Cecilia A. Roque, Geeta Gupta, and Christopher R. Lowe	43	(20)
5 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	63	(30)
6 Synthesis of Complex Carbohydrates and Glyconjugates: Enzymatic Synthesis of Globotetraose Using β-1,3-N-Acetylgalactosaminyltransferase LgtD From Haemophilus infuenzae Strain Rd
Kang Ryu, Steven Lin, Jun Shao, Jing Song, Min Chen, Wei Wang, Hanfen Li, Wen Yi, and Peng George Wang	93	(14)
7 High-Throughput Cloning for Proteomics Research
Sharon A. Doyle	107	(8)
8 Screening for the Expression of Soluble Recombinant Protein in Escherichia coil
Sharon A. Doyle	115	(8)
9 High-Throughput Purification of Hexahistidine-Tagged Proteins Expressed in E. coil
Michael B. Murphy and Sharon A. Doyle	123	(8)
10 The Wheat Germ Cell-Free Expression System: Methods for High-Throughput Materialization of Genetic Information
Tatsuya Sawasaki, Mudeppa D. Gouda, Takayasu Kawasaki, Takafumi Tsuboi, Yuzuru Tozawa, Kazuyuki Takai, and Yaeta Endo	131	(14)
11 Advances in Genome-Wide Protein Expression Using the Wheat Germ Cell-Free System
Yaeta Endo and Tatsuya Sawasaki	145	(24)
12 Production of Proteins for NMR Studies Using the Wheat Germ Cell-Free System
Toshiyuki Kohno	169	(18)
13 Adenoviral Expression of Reporter Proteins for High-Throughput Cell-Based Screening
Jon Hoyt and Randall W. King	187	(10)
14 Fabrication of Protein Function Microarrays for Systems-Oriented Proteomic Analysis
Jonathan M. Blackburn and Darren J. Hart	197	(20)
15 Peptide and Small-Molecule Microarrays
Jan Marik and Kit S. Lam	217	(10)
16 Peptide Mass Fingerprinting: Protein Identification Using MALDI-TOF Mass Spectrometry
Judith Webster and David Oxley	227	(14)
17 A Practical Protocol for Carbohydrate Microarrays
Ruobing Wang, Shaoyi Liu, Dhaval Shah, and Denong Wang	241	(12)
18 Development of a Yeast Two-Hybrid Screen for Selection of Human Ras-Raf Protein Interaction Inhibitors
Vladimir Khazak, Erica A. Golemis, and Lutz Weber	253	(20)
Index	273