Human Brain Proteome

I. Introduction........................................................................ 3 II. Transcriptomics.................................................................... 4 III. Proteomics Methodologies for Biomarker Discovery......................... 7 IV. Principles of SELDI-TOF-MS..................................................... 12 V. SELDI-TOF-MS in Clinical Proteomics Research............................. 17 VI. Biomarkers in Specific Diseases................................................. 18 VII. Metabolomics....................................................................... 25 VIII. Conclusions......................................................................... 26 References.......................................................................... 27 Proteomic Analysis of Mitochondrial Proteins Mary F. Lopez,Simon Melov,Felicity Johnson, Nicole Nagulko,Eva Golenko,Scott Kuzdzal, Suzanne Ackloo, and Alvydas Mikulskis I. Introduction........................................................................ 31 II. Model Systems...................................................................... 32 III. Technological Approaches....................................................... 33 IV. Differential Expression of Proteins in Mouse Brain Mitochondria from Cortex and Synaptosomes........................................................ 38 V. Conclusions......................................................................... 43 References.......................................................................... 44 v vi CONTENTS SECTION II PROTEOMIC APPLICATIONS NMDA Receptors, Neural Pathways, and Protein Interaction Databases Holger Husi I. Introduction ........................................................................ 51 II. NMDA Receptor.................................................................... 52 III. Molecular Clustering .............................................................. 55 IV. Signal Transduction Pathways.................................................... 61 V. Bioinformatic Analysis............................................................. 63 VI. Proteomic Databases............................................................... 67 VII. Future Directions .................................................................. 73 References........................................................................... 74 Dopamine Transporter Network and Pathways Rajani Maiya and R. Dayne Mayfield I. Introduction ........................................................................ 79 II. Structure and Function of DAT ................................................. 80 III. Cellular Localization of DAT..................................................... 81 IV. Regulation of DAT................................................................. 81 V. Mass Spectrometry-Based Proteomics........................................... 83 VI. Isolation and Validation of the DAT Proteome............................... 84 VII. Mass Spectrometry................................................................. 85 VIII. Confirmation of Members of the DAT Proteome............................. 85 IX. In Silico Analysis of DAT Proteome.............................................. 90 References........................................................................... 93 Proteomic Approaches in Drug Discovery and Development Holly D. Soares,Stephen A. Williams,Peter J. Snyder,Feng Gao, Tom Stiger,Christian Rohlff,Athula Herath,Trey Sunderland, Karen Putnam, and W. Frost White I. Proteomics in Drug Discovery and Development............................. 97 II. Using Proteomics to Identify Biomarkers of Alzheimer’s Disease: A Case Study........................................................................ 104 III. Future Challenges and Conclusions............................................. 120 References........................................................................... 121 CONTENTS vii SECTION III INFORMATICS Proteomic Informatics Steven A. Russell,William Old,Katheryn A. Resing, and Lawrence Hunter I. What is Proteomics?............................................................... 129 II. Proteomic Informatics............................................................ 131 III. Mass Spectrometry and Shotgun Proteomics.................................. 131 IV. Identifying Proteins ............................................................... 134 V. Post-hoc Validation of Protein Identification Program Output............ 139 VI. Quantification...................................................................... 141 VII. Detection of Protein Isoforms................................................... 142 VIII. Systems and Workflow Issues .................................................... 146 IX. Conclusion.......................................................................... 150 X. Appendix: List of Mentioned Algorithms by Topic.......................... 150 References.......................................................................... 154 SECTION IV CHANGES IN THE PROTEOME BY DISEASE Proteomics Analysis in Alzheimer’s Disease: New Insights into Mechanisms of Neurodegeneration D. Allan Butterfield and Debra Boyd-Kimball I. Introduction........................................................................ 161 II. Proteomics Tools .................................................................. 162 III. Proteomic Studies in AD......................................................... 170 IV. Proteomics Analysis of Transgenic Models of AD............................ 181 V. Future of Proteomics in AD ..................................................... 182 References.......................................................................... 182 Proteomics and Alcoholism Frank A. Witzmann and Wendy N. Strother I. Introduction........................................................................ 189 II. Proteomics of the Hippocampus and Nucleus Accumbens................. 192 III. Future Directions.................................................................. 203 IV. Conclusion.......................................................................... 211 References.......................................................................... 211 viii CONTENTS Proteomics Studies of Traumatic Brain Injury Kevin K. W. Wang,Andrew Ottens,William Haskins,Ming Cheng Liu, Firas Kobeissy,Nancy Denslow,SuShing Chen, and Ronald L. Hayes I. Introduction ........................................................................ 215 II. Traumatic Brain Injury............................................................ 216 III. Proteomics Analysis Overview.................................................... 221 IV. Protein Separation Methods...................................................... 221 V. Protein Identification and Quantification Methods.......................... 225 VI. TBI Proteomics Bioinformatics .................................................. 232 VII. Prospective Utilities of TBI Proteomics Data.................................. 237 References........................................................................... 237 Influence of Huntington’s Disease on the Human and Mouse Proteome Claus Zabel and Joachim Klose I. Introduction ........................................................................ 241 II. Neurodegenerative Disorders Caused by Elongated Poly-Glutamine Repeats .............................................................................. 242 III. Approach for an HD Proteomics Study ........................................ 248 IV. Materials and Methods............................................................ 248 V. Proteomics Study of HD .......................................................... 249 VI. Discussion........................................................................... 270 VII. Conclusion.......................................................................... 277 References........................................................................... 278 SECTION V OVERVIEW OF THE NEUROPROTEOME Proteomics—Application to the Brain Katrin Marcus,Oliver Schmidt,Heike Schaefer, Michael Hamacher,AndrO van Hall, and Helmut E. Meyer I. Introduction ........................................................................ 287 II. Potential of Proteomics ........................................................... 288 III. Methods in Proteome Analysis................................................... 289 IV. Proteome Analysis in Neurosciences............................................ 299 V. Administrative Realization of Neuroproteomics............................... 303 References........................................................................... 307 Index........................................................................................ 313 Contents of Recent Volumes..................................................... 325

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Cahill 7.1 Introduction 137 7.2 Technological Aspects 139 7.2.1 Protein Immobilization and Surface Chemistry 139 7.2.2 Transfer and Detection of Proteins 141 7.2.3 Chip Content 142 7.3 Applications of Protein Biochips 144 7.4 Contribution to Pharmaceutical Research and Development 150 References 151 8 Current Developments for the In Vitro Characterization of Protein Interactions 159 Daniela Moll, Bastian Zimmermann, Frank Gesellchen and Friedrich W.Herberg 8.1 Introduction 160 8.2 The Model System: cAMP-Dependent Protein Kinase 161 8.3 Real-time Monitoring of Interactions Using SPR Biosensors 161 8.4 ITC in Drug Design 163 8.5 Fluorescence Polarization, a Tool for High-Throughput Screening 165 8.6 AlphaScreen as a Pharmaceutical Screening Tool 167 8.7 Conclusions 170 References 171 9 Molecular Networks in Morphologically Intact Cells and Tissue–Challenge for Biology and Drug Development 173 Walter Schubert, Manuela Friedenberger and Marcus Bode 9.1 Introduction 173 9.2 A Metaphor of the Cell 174 9.3 Mapping Molecular Networks as Patterns: Theoretical Considerations 176 9.4 Imaging Cycler Robots 177 9.5 Formalization of Network Motifs as Geometric Objects 179 9.6 Gain of Functional Information: Perspectives for Drug Development 182 References 182 Contents IX III Applications 185 10 From Target to Lead Synthesis 187 Stefan Müllner, Holger Stark, Paivi Niskanen, Erich Eigenbrodt, SybilleMazurek and Hugo Fasold 10.1 Introduction 187 10.2 Materials and Methods 190 10.2.1 Cells and Culture Conditions 190 10.2.2 In Vitro Activity Testing 190 10.2.3 Affinity Chromatography 190 10.2.4 Electrophoresis and Protein Identification 191 10.2.5 BIAcore Analysis 191 10.2.6 Synthesis of Acyl Cyanides 192 10.2.6.1 Methyl 5-cyano-5-oxopentanoate 192 10.2.6.2 Methyl 6-cyano-6-oxohexanoate 193 10.2.6.3 Methyl-5-cyano-3-methyl-5-oxopentanoate 193 10.3 Results 193 10.4 Discussion 201 References 203 11 Differential Phosphoproteome Analysis in Medical Research 209 Elke Butt and Katrin 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