Table of Contents
Preface v
Contributors ix
Section I Introduction
1 Exploring and Profiling Protein Function with Peptide Arrays Victor E. Tapia Bernhard Ay Rudolf Volkmer 3
2 Peptide Arrays for Enzyme Profiling Alexandra Thiele Johannes Zerweck Mike Schutkowski 19
3 Using Peptide Array to Identify Binding Motifs and Interaction Networks for Modular Domains Shawn S.-C. Li Chenggang Wu 67
4 Molecular Simulations of Peptides: A Useful Tool for the Development of New Drugs and for the Study of Molecular Recognition Massimiliano Meli Giorgio Colombo 77
Section II Applications
5 Synthesis of Peptide Arrays Using SPOT-Technology and the CelluSpots-Method Dirk F.H. Winkler Kai Hilpert Ole Brandt Robert E. W. Hancock 157
6 Rapid Identification of Linear Protein Domain Binding Motifs Using Peptide SPOT Arrays Douglas J. Briant James M. Murphy Genie C. Leung Frank Sicheri 175
7 Characterization of Kinase Target Phosphorylation Consensus Motifs Using Peptide SPOT Arrays Genie C. Leung James M. Murphy Doug Briant Frank Sicheri 187
8 CelluSpots™: A Reproducible Means of Making Peptide Arrays for the Determination of SH2 Domain Binding Specificity Chenggang Wu Shawn S.-C. Li 197
9 High-Density Peptide Microarrays for Reliable Identification of Phosphorylation Sites and Upstream Kinases Alexandra Thiele Johannes Zerweck Matthias Weiwad Gunter Fischer Mike Schutkowski 203
10 Epitope Mapping of Human Chromogranin A by Peptide Microarrays Marina Cretich Renato Longhi Angelo Corti Francesco Damin Gabriele Di Carlo Valentina Sedini Marcella Chiari 221
11 Antimicrobial Peptide Arrays for Detection of Inactivated Biothreat Agents Chris R. Taitt Stella H. North Nadezhda V. Kulagina233
12 Mapping Functional Prion-Prion Protein Interaction Sites Using Prion Protein Based Peptide-Arrays Alan Rigter Jan Priem Drophatie Timmers-Parohi Jan PM Langeveld Alex Bossers 257
13 A Designed Peptide Chip: Protein Fingerprinting Technology with a Dry Peptide Array and Statistical Data Mining Kenji Usui Kin-ya Tomizaki Hisakazu Mihara 273
Section III Technological Advancements
14 Peptide Microarrays on Bisphenol A Polycarbonate Vianney Souplet Clément Roux Oleg Melnyk 287
15 Self-Assembly of PNA-Encoded Peptides into Microarrays Francois Debaene Nicolas Winssinger 299
16 A Novel Combinatorial Approach to High-Density Peptide Arrays Mario Beyer Ines Block Kai König Alexander Nesterov Simon Fernandez Thomas Felgenhauer Christopher Schirwitz Klaus Leibe Ralf F. Bischoff Frank Breitling Volker Stadler 309
17 Polypyrrole-Peptide Microarray for Biomolecular Interaction Analysis by SPR Imaging Marie-Bernadette Villiers Sandra Cortès Carine Brakha Patrice Marche André Roget Thierry Livache 317
18 The Peptide Microarray-Based Assay for Kinase Functionality and Inhibition Study Zhenxin Wang 329
19 An Advanced Application of Protein Microarrays: Cell-Based Assays for Functional Genomics Roberta Carbone 339
20 Profiling the Autoantibody Repertoire by Screening Phage-Displayed Human cDNA Libraries Roberto Di Niro Sara D'Angelo Paola Secco Roberto Marzari Claudio Santoro Daniele Sblattero 353
Section IV Software/Web Tools and Data Analysis
21 Visualisation and Pre-processing of Peptide Microarray Data Marie Reilly Davide Valentini 373
22 Web-Based Design of Peptide Microarrays Using ?PepArray Pro Tongbin Li Zhixiang Zuo Qi Zhu Ailing Hong Xiaochuan Zhou Xiaolian Gao 391
23 Qualitative and Quantitative Analysis of Peptide Microarray Binding Experiments Using SVM-PEPARRAY Gang Chen Zhixiang Zuo Qi Zhu Ailing Hong Xiaochuan Zhou Xiaolian Gao Tongbin Li 403
24 PASE: A Web-Based Platform for Peptide/Protein Microarray Experiments Fabien Pamelard Gael Even Costin Apostol Cristian Preda Clarisse Dhaenens Vronique Fafeur Rémi Desmet Oleg Melnyk 413
Index 431
