Cell junctions: adhesion, development, and disease
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2008
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| 245 | 1 | 0 | |a Cell junctions |b adhesion, development, and disease |c ed. by Susan E. LaFlamme ... |
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| 300 | |a XV, 301 S. |b Ill., graph. Darst. | ||
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| 650 | 7 | |a Cytoadherence |2 cabt | |
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Datensatz im Suchindex
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I VII
Contents
Preface V
List of Contributors XIII
Part One Cell-Matrix Junctions
1 The Ins and Outs of Integrin Signaling 3
Asoka Banno and Mark H. Ginsberg
1.1 General Overview 3
1.1.1 Integrin Receptors 3
1.1.2 Functions 4
1.2 Integrin Activation 5
1.2.1 Definition 5
1.2.1.1 Platelets 6
1.2.1.2 Leukocytes 6
1.2.2 Structural Basis of Activation 6
1.2.2.1 Extracellular Rearrangements 7
1.2.2.2 Transmembrane Propagation 7
1.2.2.3 Intracellular Rearrangements 8
1.2.2.4 Interactions at the Integrin Cytoplasmic Domains 9
1.2.3 Regulation of Integrin Activation 13
1.2.4 Future Research Directions 16
References 18
2 Integrin Signaling Through Focal Adhesion Kinase 25
Youngdong Yoo andJun-Lin Guan
2.1 Introduction 25
2.2 Structure of FAK 26
2.3 Regulation of FAK Activity 28
2.3.1 Activation of FAK 28
2.3.2 Inhibition of FAK Activity 30
2.4 Regulation of Cellular Functions by FAK Signaling Pathways 30
2.4.1 Cell Adhesion and Spreading 31
2.4.2 Cell Migration and Invasion 32
Cell junctions. Adhesion, Development, and Disease.
Edited by Susan E. LaFlamme and Andrew Kowakzyk
Copyright © 2008 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978-3-527-31882-7
VIII I Contents
2.4.3 Cell Survival and Proliferation 36
2.5 Recent Analysis of FAK Functions In Vivo 37
2.6 Conclusions 39
Acknowledgment 39
References 39
3 The Paxillin Family and Tissue Remodeling 47
David A. Tumbarello and Christopher E. Turner
3.1 Focal Adhesions and the Paxillin Superfamily 47
3.1.1 Focal Adhesions 47
3.1.2 The Paxillin Superfamily 49
3.1.3 Structure of Paxillin 50
3.1.4 Structure of Hic-5 51
3.2 The Paxillin Superfamily and Tissue Remodeling 52
3.2.1 Epithelial-Mesenchymal Transformation 52
3.2.2 Integrin-Mediated Signaling and EMT 53
3.2.3 Paxillins a and 8 in EMT 56
3.2.4 Hic-5 and EMT 58
References 60
4 Adhesion Dynamics in Motile Cells 77
Christa L Cortesio, Keefe T. Chan, and Anna Huttenlocher
4.1 Introduction 71
4.2 Focal Adhesion Dynamics 72
4.2.1 Focal Adhesion Composition 73
4.2.2 Mechanisms of Focal Adhesion Assembly 74
4.2.2.1 Rho GTPases 75
4.2.2.2 Talin and Phosphoinositides 75
4.2.3 Mechanisms of Focal Adhesion Disassembly 75
4.2.3.1 Calpain 76
4.2.3.2 Tyrosine Phosphorylation and Contractile Machinery 76
4.3 Podosome and Invadopodia Dynamics 76
4.3.1 Podosome and Invadopodia Architecture 77
4.3.2 Molecular Mechanisms of PTA Assembly 78
4.3.2.1 Actin Regulatory Proteins 78
4.3.2.2 Rho GTPases 79
4.3.2.3 Signaling Molecules 79
4.3.3 Molecular Mechanisms of PTA Disassembly 80
4.4 Summary 80
Acknowledgments 81
References 81
5 Integrin Trafficking 89
Susan E. LaFlamme, Feng Shi, and Jane Sottile
5.1 Introduction 89
Contents I IX
5.2 Historical Perspective 89
5.3 Clathrin versus Lipid Rafts 90
5.4 Internalization of Occupied versus Unoccupied Integrins 91
5.5 Regulation of Integrin Trafficking 92
5.6 The Role of Integrin Cytoplasmic Domains 94
5.7 Integrin-Dependent Endocytosis of Microbial Pathogens 95
5.8 Regulation of Cell Adhesion and Migration by Integrin
Trafficking 96
5.9 The Regulation of Integrin Trafficking by Cell Adhesion 96
5.10 Integrin Trafficking and ECM Remodeling 98
5.11 Conclusions 100
Acknowledgments 101
References 101
6 Hemidesmosomes and their Components: Adhesion versus Signaling
in Health and Disease 709
Kristina Kligys, Kev'm Hamill, and Jonathan C. R.Jones
6.1 Introduction 109
6.2 The Structural Components of the Hemidesmosome 110
6.2.1 The Plaque Proteins 110
6.2.1.1 Plectin 110
6.2.1.2 BP23O 112
6.2.2 Membrane Elements 112
6.2.2.1 a6(34 Integrin 112
6.2.2.2 BP180 314
6.2.2.3 CD151 115
6.3 Laminin-332 115
6.4 Hemidesmosome Assembly and Disassembly 3 36
6.5 Hemidesmosomes and Disease 118
6.5.1 Inherited Skin Diseases Involving Hemidesmosome Proteins 118
6.5.1.1 Disease Involving 0(6(54 Integrin 118
6.5.1.2 Disease Involving Plectin 119
6.5.1.3 Disease Involving BP180 119
6.5.1.4 Disease Involving CD151 120
6.5.1.5 Disease Involving Laminin-332 120
6.5.2 Autoimmmune Diseases Associated with Hemidesmosomes 121
6.5.2.1 BP and Related Diseases 121
6.5.2.2 Cicatricial Pemphigoid 122
6.5.2.3 Autoimmune Diseases Involving a6(}4 Integrin 122
6.6 a6|34 Integrin and Laminin-332 Expression in Cancer 123
6.7 Signaling by the a6(34 Integrin in Pathological States and
Wound Healing 123
6.8 Laminin-332, a6(i4 Integrin and Migration 125
6.9 Conclusions 326
References 126
X I Contents
7 Cell Matrix Adhesion in Three Dimensions 735
Patricia J. Keely
7.1 Introduction 135
7.2 Model 3D Matrices for Investigations of Cell Behavior 136
7.2.1 Matrigel/Reconstituted Basement Membrane (rBM) 136
7.2.2 Collagen Gels 136
7.2.3 Fibrin Gels 138
7.2.4 Cell-Derived Fibronectin-Based Matrices 138
7.2.5 Engineered 3D Matrices and Microfluidic Chambers 138
7.3 Cell Behavior and Adhesive Structures Differ between 3D and 2D
Matrices 139
7.4 "Compliancy" or Elastic Modulus Determines Cellular Response to
ECMs 140
7 A.I Cellular Contractility and the Response to Matrix Compliance 141
7.4.2 Rho Regulates the Cytoskeleton and Contractility 141
7 A3 Rho/ROCK, Contractility, and Focal Adhesion Formation 142
7AA Focal Adhesions as Transducers of Biophysical Signals 143
7.5 A Model for Cellular Response to 3D Matrices Varying in
Compliance 144
Acknowledgments 146
References 146
Part Two Cell-Cell Junctions
8 Armadillo Repeat Proteins at Epithelial Adherens Junctions 753
Laura J. Lewis-Tujfin and Panos Z. Anastasiadis
8.1 Introduction 153
8.2 P-Catenin 156
8.3 Plakoglobin 158
8.4 pl20-Catenin 159
8.5 The Role of Armadillo Repeat Proteins and AJs in Cancer 163
8.6 Conclusions 165
References 165
9 Signaling To and Through The Endothelial Adherens Junction 769
Deana M. Ferreri and Peter A. Vincent
9.1 Introduction 169
9.2 Cadherins 170
9.2.1 VE-Cadherin Extracellular Domain 173
9.2.2 Interaction of Cadherin Cytoplasmic Domain and Catenins 174
9.2.2.1 VE-Cadherin Juxtamembrane Region and pl20 174
9.2.2.2 VE-Cadherin Catenin Binding Domain 176
9.3 Phosphorylation and Junction Assembly/Disassembly 179
9.3.1 Tyrosine Phosphorylation of Endothelial AJ Proteins 180
9.3.2 Serine/Threonine Phosphorylation of Endothelial AJ Proteins 182
9.4 Small GTPases and Junction Assembly 183
Contents XI
9.4.1 Rho GTPases 183
9.4.2 Rapl GTPase 186
9.5 Conclusions 187
References 187
10 Cap Junctions: Connexin Functions and Roles in Human Disease 197
Michael Koval
10.1 Introduction 197
10.2 Connexin Structure and Assembly 198
10.3 Interactions Between Different Connexins 199
10.4 Connexin Binding Proteins and Phosphorylation 201
10.5 Channel Permeability and Signaling 202
10.6 Connexins in Human Disease 203
10.7 Role of Connexins in Vessel Inflammation and Atherosclerosis 206
10.8 Conclusions 207
References 208
11 Tight Junctions in Simple and Stratified Epithelium 277
Cara J. Gottardi and Carien M. Niessen
11.1 Introduction 217
11.2 Ultrastructure of Tight Junctions 238
11.3 Tight Junctions and Epithelial Barrier Function 219
11.3.1 Transmembrane Components 219
11.3.2 Scaffolding Proteins 221
11.3.3 Actin and Related Cytoskeleton Proteins 221
11.4 Regulation of Tight Junction Barrier Function 222
11.5 Tight Junctions and Epithelial Polarity 222
11.5.1 Par3/Par6/aPKC Complex 223
11.5.2 Crbs/Patj/Pals 223
11.5.3 Fence Function 224
11.6 Signaling from Tight Junctions: Coupling Junction Maturation to
Transcription-Mediated Differentiation 225
11.7 Tight Junctions in Stratifying Epithelia 225
11.8 Tight Junctions and Disease 227
11.9 Concluding Remarks 228
Acknowledgments 229
References 229
12 Desmosomes in Development and Disease 235
Ansgar Schmidt and Peter J. Koch
12.1 Introduction 235
12.2 Molecular Composition of Desmosomes, Disease Associations, and
Animal Models 236
12.2.1 Desmosomal Cadherins 236
12.2.2 Desmoplakin 240
12.3 Plakoglobin 240
XIII Contents
12.4 Plakophilins 242
12.5 Accessor)' Desmosomal Proteins 24i
12.6 Desmosomal Proteins in Embryonic Development 243
12.7 Concluding Remarks 244
Acknowledgments 245
References 245
13 Cadherin Trafficking and Junction Dynamics 257
Christine M. Chiasson and Andrew P. Kowalczyk
13.1 Introduction 251
13.2 Exocytosis and Polarized Sorting of Adherens |unction Proteins 252
13.3 Endocytosis of Adherens Junction Proteins 255
13.4 Catenin Regulation of Cadherin Endocytosis 258
13.5 Rho GTPase Regulation of Cadherin Endocytosis 261
13.6 Co-Regulation of Cadherin and Receptor Tyrosine Kinase Function by
Endocytosis 262
13.7 Conclusions 264
Acknowledgments 266
References 266
Part Three Cell-Matrix and Cell-Cell Crosstalk
14 Crosstalk Between Cell-Cell and Cell-Matrix Adhesion 273
C. Michael DiPenio
14.1 Introduction 273
14.1.1 Coordinate Regulation of Cell-Cell and Cell-Matrix Adhesion 273
14.1.2 Crosstalk Between Integrins and Cadherins 274
14.2 Mechanisms of Integrin-Cadherin Crosstalk 275
14.2.1 Extracellular Proteolysis 275
14.2.2 Cross-Regulation of Gene Expression 277
14.2.3 Changes in Intracellular Force Generation 278
14.2.4 Integrin-Cadherin Associations at Sites of Cell Adhesion 279
14.2.5 Intracellular Signal Transduction Pathways 281
14.2.5.1 FAK: An Integrin Effector that Signals to Cadherins 282
14.2.5.2 Fer: A Tyrosine Kinase that Translocates between Cadherins and
Integrins 282
14.2.5.3 Rapl: A Central Regulator of Integrin-Cadherin Crosstalk
Pathways? 283
14.2.5.4 The Epidermis as a Model for Investigating Cadherin-Integrin
Crosstalk 285
14.3 Future Prospects 286
Acknowledgments 287
References 287
Index 295
Contents XIII
6.2.3 Summary 215
6.2.4 Perspectives 215
6.2.5 Sample Preparation: Short Protocol 215
6.2.5.1 Recommended Equipment and Consumables 215
6.2.5.2 Preparation of the Source Plate 216
6.2.5.3 Spotting 217
6.2.5.4 Cell Culture and Experiment 217
References 218
6.3 Sample Preparation by Laser Microdissection and Catapulting
for Proteome Analysis 219
Karin Schutze, Andrea Buchstaller, Yilmaz Niyaz, Christian Melle,
Gunther Ernst, Kerstin David, Thorsten Schlomm,
and Ferdinand von Eggeling
6.3.1 Introduction: Laser Microdissection and Functional Proteomic
Research 219
6.3.2 The Relevance of Pure Starring Material for Proteomics 219
6.3.3 Examples of Combined LMPC and Proteomic Analyses 220
6.3.3.1 LMPC and Preeclampsia 220
6.3.3.2 LMPC and Renal Cell Carcinoma 221
6.3.3.3 LMPC and Hepatocellular Carcinoma 221
6.3.3.4 LMPC and Brain Disorders 221
6.3.3.5 LMPC and Plant Biology 221
6.3.4 LMPC Adapted for Proteomic Applications 222
6.3.5 LMPC Combined with SELDI-TOF MS: A Promising Approach
for Patient-Specific Analyses 224
6.3.6 Correlation of Gene and Protein Expression: The Best Data
Capture for Comprehensive Diagnosis 228
6.3.7 Recipe for Beginners 228
6.3.7.1 Patients and Specimens 228
6.3.7.2 Laser Microdissection of Tissue Sections 230
6.3.7.3 ProteinChip Array Preparation and Analysis 230
6.3.8 Summary and Outlook 231
References 232
6.4 Sample Preparation for Flow Cytometry 234
Derek C. Davies
6.4.1 Introduction 234
6.4.2 Sample Preparation for Flow Cytometry 236
6.4.2.1 Preparation from Cells in Suspension 236
6.4.2.2 Preparation from Adherent Cells 237
6.4.2.3 Preparation from Solid Tissue 237
6.4.2.4 General Considerations 237
6.4.3 Identification of Relevant Cells 238
6.4.4 Cell Sorting 238
6.4.4.1 Cells and Samples 238
6.4.4.2 Cytometer Considerations 239
XIV Contents
6.4.5 Application Example 240
6.4.6 Summary 242
6.4.7 Perspectives 242
6.4.8 Recipes for Beginners 242
6.4.8.1 Cultured Suspension Cells 242
6.4.8.2 Adherent Cells 242
6.4.8.3 Solid Tissue 243
References 243
7 Chromatography 245
7.1 Sample Preparation for HPLC-Based Proteome Analysis 245
Egidijus Machtejevas and Klaus K. Unger
7.1.1 Introduction 245
7.1.2 Problems Related to Direct Sample Injection in HPLC 246
7.1.3 Trial and Error Selection of the Sample Preparation Method 247
7.1.4 Classical Approaches 249
7.1.5 Specific Approaches Applied to Sample Clean-Up in Proteomics 250
7.1.5.1 Miniaturized Extraction Techniques 250
7.1.5.2 Most Abundant Component Depletion 250
7.1.5.3 Affinity-Enrichment Approaches 251
7.1.6 On-line Sample Clean-Up Approaches 252
7.1.7 Restricted Access Technology 254
7.1.8 Application Example: The Case Study 259
7.1.9 Conclusion and Perspectives 260
References 262
7.2 Sample Preparation for Two-Dimensional Phosphopeptide
Mapping and Phosphoamino Acid Analysis 265
Anamarija Kruljac-Letunic and Andree Blaukat
7.2.1 Introduction 265
7.2.2 Important Aspects in Sample Preparation Procedures 265
7.2.3 Application Example 267
7.2.4 Summary 267
7.2.5 Perspective 269
7.2.6 Recipe for Beginners 269
7.2.6.1 2-D Phosphopeptide Mapping Procedure 269
7.2.6.2 Phosphoamino Acid Analysis Procedure 271
References 271
8 Structural Proteomics 273
8.1 Exploring Protein-Iigand Interactions by Solution NMR 273
Rudolf Hartmann, Thomas Slangier, Bernd W.Konig,
and Dieter Willbold
8.1.1 Introduction 273
8.1.2 Localization of Interaction Sites by Chemical Shift Perturbation
(CSP) Mapping 274
Contents XV
8.1.3 Saturation Transfer Difference Spectroscopy 276
8.1.4 Iigand Screening by NMR 278
References 279
8.2 Sample Preparation for Crystallography 281
Djordje Musil
8.2.1 Introduction 281
8.2.2 Use of Recombinant Proteins in Crystallization 282
8.2.3 Protein Solubility and Crystallization 284
8.2.4 Protein Crystallization 286
8.2.5 Practical Examples 291
References 292
9 Interaction Analysis 295
9.1 Sample Preparation for Protein Complex Analysis by the
Tandem Affinity Purification (TAP) Method 295
Bertrand Siraphin and Andrzej Dziembowski
9.1.1 Introduction 295
9.1.2 The Problem with Regards to Sample Preparation:
The Pros and the Cons 296
9.1.3 Application Example 300
9.1.4 Summary 301
9.1.5 Perspective 301
9.1.6 Recipe for Beginners 301
References 302
9.2 Exploring Membrane Proteomes 303
Filippa Stenberg and Daniel O. Daley
9.2.1 Introduction 303
9.2.2 Defining Membrane Proteomes 303
9.2.3 Separation of Membrane Proteomes 304
9.2.4 Experimental Identification of Membrane Proteins 307
9.2.5 Mapping Membrane Interactomes 307
9.2.6 Structural Analysis of Membrane Proteomes 308
9.2.7 Summary and Perspective 309
9.2.8 Recipe for Beginners 311
9.2.8.1 Sample Preparation 311
9.2.8.2 BN-PAGE 311
9.2.8.3 SDS-PAGE 312
References 312
10 Post-Translational Modifications 317
10.1 Sample Preparation for Phosphoproteome Analysis 317
Rent P. Zahedi and Albert Sickmann
10.1.1 Introduction 317
10.1.2 General Sample Preparation 317
XVI Contents
10.1.3 Reduction of Sample Complexity 318
10.1.3.1 Gel Electrophoresis 318
10.1.3.2 Isoelectric Focusing 318
10.1.4 Methods for Phosphopeptide/Protein Enrichment 319
10.1.4.1 Immunoprecipitation 319
10.1.4.2 Immobilized Metal Ion Affinity Chromatography (IMAC) 319
10.1.4.3 Metal Oxides 320
10.1.4.4 Cation-Exchange Chromatography 321
10.1.4.5 Derivatization Approaches 322
10.1.5 Summary 323
10.1.6 Perspective 324
10.1.7 Recipe for Beginners: IMAC 324
References 325
10.2 Sample Preparation for Analysis of Post-Translarional
Modifications: Glycosylation 328
David S. Selby, Martin R. Larsen, MirenJ. Omaetxebarria,
and Peter Roepstorff
10.2.1 Introduction 328
10.2.2 Advantages and Disadvantages of Different Sample
Preparation Methods 331
10.2.3 Example Applications of Enrichment Methods 334
10.2.3.1 ZIC-HILIC Microcolumns for Preparation of N-Linked
Glycan-Containing Samples 334
10.2.3.2 Titanium Dioxide Microcolumns for Enrichment of Sialic
Acid-Containing Glycopeptides and Glycosylphosphatidylinositol
lipid-Anchored Peptides 336
10.2.4 Summary 337
10.2.5 Perspective 338
10.2.6 Recipe for Beginners: Enrichment of Glycopeptides with a
HILIC Microcolumn 338
10.2.6.1 Materials 338
10.2.6.2 Procedure: Purification of Glycopeptides 339
10.2.6.3 Procedure: Deglycosylation of N-Linked Glycopeptides 339
References 340
11 Species-Dependent Proteomics 343
11.1 Sample Preparation and Data Processing in Plant Proteomics 343
Katja Baerenfaller, Wilhelm Cruissem, and Sacha Baginsky
11.1.1 Introduction 343
11.1.2 Plant-Specific Considerations in Proteomics 344
11.1.2.1 Cell Walls 344
11.1.2.2 Plasrids 344
11.1.2.3 Protein Extraction from Plant Tissue 345
11.1.2.4 Extraction from Recalcitrant and Resistant Tissue 345
Contents XVII
11.1.2.5 Dynamic Range limitations 346
11.1.2.6 Proteomics in As-Yet Unsequenced Organisms 346
11.1.3 Sample Preparation Protocols 347
11.1.3.1 Cell Wall Protein Extraction 348
11.1.3.2 Plastid Isolation 349
11.1.3.3 Protein Extraction with TCA/Acetone 350
11.1.3.4 Phenol Extraction 351
11.1.3.5 Serial Extraction 351
11.1.3.6 Extraction from Recalcitrant and Resistant Tissue 352
11.1.3.7 Extraction and Fractionation with Polyethylene Glycol (PEG) 353
11.1.3.8 Stages Following Protein Extraction 353
11.1.4 MS/MS Data Processing for Unsequenced Organisms 354
11.1.5 Concluding Remarks 355
References 356
11.2 Sample Preparation for MudPIT with Bacterial Protein Samples 358
Ansgar Poetsch and Dirk Wolters
11.2.1 Introduction 358
11.2.2 The MudPIT Technology 359
11.2.3 Membrane Proteins and MudPIT 361
11.2.4 Quantitative MudPIT 363
11.2.5 Limitations of MudPIT 364
11.2.6 Pitfalls of MudPIT 365
11.2.7 Summary 365
11.2.8 Perspective 365
11.2.9 Recipe for Beginners: MudPIT: Soluble and Membrane Proteins 366
References 368
11.3 Sample Preparation for the Cell-Wall Proteome Analysis of Yeast
and Fungi 371
Kai Sohn, Ekkehard Hitler, and Steffen Rupp
11.3.1 Introduction 371
11.3.2 Description of the Problem with Regards to Sample Preparation 372
11.3.3 Application Example 373
11.3.4 Summary 375
11.3.5 Perspective 376
11.3.6 Recipe for Beginners 376
11.3.6.1 Cultures 376
11.3.6.2 Preparation of Soluble Cell-Surface Proteins 376
11.3.6.3 Preparation of Peptides from Covalently Linked Cell-Wall Proteins 377
References 378
12 The Human Proteosome 379
12.1 Clinical Proteomics: Sample Preparation and Standardization 379
Cerd Schmitz and Carsten Gnewuch
12.1.1 Introduction 379
XVIII Contents
12.1.2 The Preanalytical Phase: Sample Preparation, Standardization,
and Quality Management 380
12.1.2.1 Standardization of the (Pre)-Analytical Process 381
12.1.3 Proteomics in Body Fluids 382
12.1.3.1 Techniques for Proteomic Analysis 382
12.1.3.2 Applications 383
12.1.3.3 Preparation of Clinical Samples for Fluidic Proteomics 386
12.1.4 Cellular Proteomics (Cytomics) 389
12.1.4.1 Sample Preparation and Standardization for Clinical Cytomics 389
12.1.4.2 Tissue Arrays 390
12.1.4.3 Bead-Based Immunoassays for Protein Analysis 391
12.1.4.4 Preparative Methods 391
12.1.4.5 Clinical Applications in Cytomics 399
12.1.5 Conclusion 404
References 405
12.2 Stem Cell Proteomics 412
Regina Ebert, Cabriele Miiller, Jerzy Aclamski, and Franz Jakob
12.2.1 Introduction 412
12.2.2 Stem Cell Niches 413
12.2.3 Why Study Proteomes in Stem Cells? 413
12.2.4 Technical Challenges and Problems 414
12.2.4.1 Stem Cell Preparation 414
12.2.4.2 Cultivation 415
12.2.4.3 Treatment 415
12.2.4.4 Whole-Cell Proteome 415
12.2.4.5 Secretory Proteome 415
12.2.5 Recipes for Beginners 417
12.2.5.1 Whole-Cell Lysate 417
12.2.5.2 Secretory Proteome Procedure 418
12.2.5.3 Labeling with 35S 418
12.2.5.4 Ethanol Precipitation 419
12.2.5.5 TCA Precipitation 419
References 419
13 Bioinformatics 423
13.1 Bioinformatics Support for Mass Spectrometric Quality Control 423
Knut Reinert, Tim Conrad, and Oliver Kohlbacher
13.1.1 Introduction 423
13.1.2 Problem description 423
13.1.2.1 Signal Processing Pitfalls 424
13.1.2.2 Map Quality Control 425
13.1.2.3 Statistical Validation Results 425
13.1.3 Quality Assessment for One-Dimensional (1-D) MS Data 426
13.1.3.1 Filter 427
Contents I XIX
13.1.4 Application Example: Absolute Quantification of an Unknown
Peptide Content 428
13.1.5 Summary 429
13.1.6 Perspective 430
13.1.7 Recipe for Beginners 430
13.1.7.1 Acquiring the Raw Data 430
13.1.7.2 Preprocessing the Data 431
13.1.7.3 Analyzing the Preprocessed Data 431
References 431
13.2 Use of Physico-Chemical Properties in Peptide and Protein
Identification 433
Anastasia K. Yocum, PeterJ. Ulintz, and Philip C. Andrews
13.2.1 Introduction 433
13.2.2 Isoelectric Point 434
13.2.3 Ion-Exchange Chromatography 436
13.2.4 Reversed-Phase Chromatography 438
13.2.5 Mass Accuracy 442
13.2.6 Summary 443
References 444
Index 449 |
| adam_txt |
I VII
Contents
Preface V
List of Contributors XIII
Part One Cell-Matrix Junctions
1 The Ins and Outs of Integrin Signaling 3
Asoka Banno and Mark H. Ginsberg
1.1 General Overview 3
1.1.1 Integrin Receptors 3
1.1.2 Functions 4
1.2 Integrin Activation 5
1.2.1 Definition 5
1.2.1.1 Platelets 6
1.2.1.2 Leukocytes 6
1.2.2 Structural Basis of Activation 6
1.2.2.1 Extracellular Rearrangements 7
1.2.2.2 Transmembrane Propagation 7
1.2.2.3 Intracellular Rearrangements 8
1.2.2.4 Interactions at the Integrin Cytoplasmic Domains 9
1.2.3 Regulation of Integrin Activation 13
1.2.4 Future Research Directions 16
References 18
2 Integrin Signaling Through Focal Adhesion Kinase 25
Youngdong Yoo andJun-Lin Guan
2.1 Introduction 25
2.2 Structure of FAK 26
2.3 Regulation of FAK Activity 28
2.3.1 Activation of FAK 28
2.3.2 Inhibition of FAK Activity 30
2.4 Regulation of Cellular Functions by FAK Signaling Pathways 30
2.4.1 Cell Adhesion and Spreading 31
2.4.2 Cell Migration and Invasion 32
Cell junctions. Adhesion, Development, and Disease.
Edited by Susan E. LaFlamme and Andrew Kowakzyk
Copyright © 2008 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978-3-527-31882-7
VIII I Contents
2.4.3 Cell Survival and Proliferation 36
2.5 Recent Analysis of FAK Functions In Vivo 37
2.6 Conclusions 39
Acknowledgment 39
References 39
3 The Paxillin Family and Tissue Remodeling 47
David A. Tumbarello and Christopher E. Turner
3.1 Focal Adhesions and the Paxillin Superfamily 47
3.1.1 Focal Adhesions 47
3.1.2 The Paxillin Superfamily 49
3.1.3 Structure of Paxillin 50
3.1.4 Structure of Hic-5 51
3.2 The Paxillin Superfamily and Tissue Remodeling 52
3.2.1 Epithelial-Mesenchymal Transformation 52
3.2.2 Integrin-Mediated Signaling and EMT 53
3.2.3 Paxillins a and 8 in EMT 56
3.2.4 Hic-5 and EMT 58
References 60
4 Adhesion Dynamics in Motile Cells 77
Christa L Cortesio, Keefe T. Chan, and Anna Huttenlocher
4.1 Introduction 71
4.2 Focal Adhesion Dynamics 72
4.2.1 Focal Adhesion Composition 73
4.2.2 Mechanisms of Focal Adhesion Assembly 74
4.2.2.1 Rho GTPases 75
4.2.2.2 Talin and Phosphoinositides 75
4.2.3 Mechanisms of Focal Adhesion Disassembly 75
4.2.3.1 Calpain 76
4.2.3.2 Tyrosine Phosphorylation and Contractile Machinery 76
4.3 Podosome and Invadopodia Dynamics 76
4.3.1 Podosome and Invadopodia Architecture 77
4.3.2 Molecular Mechanisms of PTA Assembly 78
4.3.2.1 Actin Regulatory Proteins 78
4.3.2.2 Rho GTPases 79
4.3.2.3 Signaling Molecules 79
4.3.3 Molecular Mechanisms of PTA Disassembly 80
4.4 Summary 80
Acknowledgments 81
References 81
5 Integrin Trafficking 89
Susan E. LaFlamme, Feng Shi, and Jane Sottile
5.1 Introduction 89
Contents I IX
5.2 Historical Perspective 89
5.3 Clathrin versus Lipid Rafts 90
5.4 Internalization of Occupied versus Unoccupied Integrins 91
5.5 Regulation of Integrin Trafficking 92
5.6 The Role of Integrin Cytoplasmic Domains 94
5.7 Integrin-Dependent Endocytosis of Microbial Pathogens 95
5.8 Regulation of Cell Adhesion and Migration by Integrin
Trafficking 96
5.9 The Regulation of Integrin Trafficking by Cell Adhesion 96
5.10 Integrin Trafficking and ECM Remodeling 98
5.11 Conclusions 100
Acknowledgments 101
References 101
6 Hemidesmosomes and their Components: Adhesion versus Signaling
in Health and Disease 709
Kristina Kligys, Kev'm Hamill, and Jonathan C. R.Jones
6.1 Introduction 109
6.2 The Structural Components of the Hemidesmosome 110
6.2.1 The Plaque Proteins 110
6.2.1.1 Plectin 110
6.2.1.2 BP23O 112
6.2.2 Membrane Elements 112
6.2.2.1 a6(34 Integrin 112
6.2.2.2 BP180 314
6.2.2.3 CD151 115
6.3 Laminin-332 115
6.4 Hemidesmosome Assembly and Disassembly 3 36
6.5 Hemidesmosomes and Disease 118
6.5.1 Inherited Skin Diseases Involving Hemidesmosome Proteins 118
6.5.1.1 Disease Involving 0(6(54 Integrin 118
6.5.1.2 Disease Involving Plectin 119
6.5.1.3 Disease Involving BP180 119
6.5.1.4 Disease Involving CD151 120
6.5.1.5 Disease Involving Laminin-332 120
6.5.2 Autoimmmune Diseases Associated with Hemidesmosomes 121
6.5.2.1 BP and Related Diseases 121
6.5.2.2 Cicatricial Pemphigoid 122
6.5.2.3 Autoimmune Diseases Involving a6(}4 Integrin 122
6.6 a6|34 Integrin and Laminin-332 Expression in Cancer 123
6.7 Signaling by the a6(34 Integrin in Pathological States and
Wound Healing 123
6.8 Laminin-332, a6(i4 Integrin and Migration 125
6.9 Conclusions 326
References 126
X I Contents
7 Cell Matrix Adhesion in Three Dimensions 735
Patricia J. Keely
7.1 Introduction 135
7.2 Model 3D Matrices for Investigations of Cell Behavior 136
7.2.1 Matrigel/Reconstituted Basement Membrane (rBM) 136
7.2.2 Collagen Gels 136
7.2.3 Fibrin Gels 138
7.2.4 Cell-Derived Fibronectin-Based Matrices 138
7.2.5 Engineered 3D Matrices and Microfluidic Chambers 138
7.3 Cell Behavior and Adhesive Structures Differ between 3D and 2D
Matrices 139
7.4 "Compliancy" or Elastic Modulus Determines Cellular Response to
ECMs 140
7 A.I Cellular Contractility and the Response to Matrix Compliance 141
7.4.2 Rho Regulates the Cytoskeleton and Contractility 141
7 A3 Rho/ROCK, Contractility, and Focal Adhesion Formation 142
7AA Focal Adhesions as Transducers of Biophysical Signals 143
7.5 A Model for Cellular Response to 3D Matrices Varying in
Compliance 144
Acknowledgments 146
References 146
Part Two Cell-Cell Junctions
8 Armadillo Repeat Proteins at Epithelial Adherens Junctions 753
Laura J. Lewis-Tujfin and Panos Z. Anastasiadis
8.1 Introduction 153
8.2 P-Catenin 156
8.3 Plakoglobin 158
8.4 pl20-Catenin 159
8.5 The Role of Armadillo Repeat Proteins and AJs in Cancer 163
8.6 Conclusions 165
References 165
9 Signaling To and Through The Endothelial Adherens Junction 769
Deana M. Ferreri and Peter A. Vincent
9.1 Introduction 169
9.2 Cadherins 170
9.2.1 VE-Cadherin Extracellular Domain 173
9.2.2 Interaction of Cadherin Cytoplasmic Domain and Catenins 174
9.2.2.1 VE-Cadherin Juxtamembrane Region and pl20 174
9.2.2.2 VE-Cadherin Catenin Binding Domain 176
9.3 Phosphorylation and Junction Assembly/Disassembly 179
9.3.1 Tyrosine Phosphorylation of Endothelial AJ Proteins 180
9.3.2 Serine/Threonine Phosphorylation of Endothelial AJ Proteins 182
9.4 Small GTPases and Junction Assembly 183
Contents XI
9.4.1 Rho GTPases 183
9.4.2 Rapl GTPase 186
9.5 Conclusions 187
References 187
10 Cap Junctions: Connexin Functions and Roles in Human Disease 197
Michael Koval
10.1 Introduction 197
10.2 Connexin Structure and Assembly 198
10.3 Interactions Between Different Connexins 199
10.4 Connexin Binding Proteins and Phosphorylation 201
10.5 Channel Permeability and Signaling 202
10.6 Connexins in Human Disease 203
10.7 Role of Connexins in Vessel Inflammation and Atherosclerosis 206
10.8 Conclusions 207
References 208
11 Tight Junctions in Simple and Stratified Epithelium 277
Cara J. Gottardi and Carien M. Niessen
11.1 Introduction 217
11.2 Ultrastructure of Tight Junctions 238
11.3 Tight Junctions and Epithelial Barrier Function 219
11.3.1 Transmembrane Components 219
11.3.2 Scaffolding Proteins 221
11.3.3 Actin and Related Cytoskeleton Proteins 221
11.4 Regulation of Tight Junction Barrier Function 222
11.5 Tight Junctions and Epithelial Polarity 222
11.5.1 Par3/Par6/aPKC Complex 223
11.5.2 Crbs/Patj/Pals 223
11.5.3 Fence Function 224
11.6 Signaling from Tight Junctions: Coupling Junction Maturation to
Transcription-Mediated Differentiation 225
11.7 Tight Junctions in Stratifying Epithelia 225
11.8 Tight Junctions and Disease 227
11.9 Concluding Remarks 228
Acknowledgments 229
References 229
12 Desmosomes in Development and Disease 235
Ansgar Schmidt and Peter J. Koch
12.1 Introduction 235
12.2 Molecular Composition of Desmosomes, Disease Associations, and
Animal Models 236
12.2.1 Desmosomal Cadherins 236
12.2.2 Desmoplakin 240
12.3 Plakoglobin 240
XIII Contents
12.4 Plakophilins 242
12.5 Accessor)' Desmosomal Proteins 24i
12.6 Desmosomal Proteins in Embryonic Development 243
12.7 Concluding Remarks 244
Acknowledgments 245
References 245
13 Cadherin Trafficking and Junction Dynamics 257
Christine M. Chiasson and Andrew P. Kowalczyk
13.1 Introduction 251
13.2 Exocytosis and Polarized Sorting of Adherens |unction Proteins 252
13.3 Endocytosis of Adherens Junction Proteins 255
13.4 Catenin Regulation of Cadherin Endocytosis 258
13.5 Rho GTPase Regulation of Cadherin Endocytosis 261
13.6 Co-Regulation of Cadherin and Receptor Tyrosine Kinase Function by
Endocytosis 262
13.7 Conclusions 264
Acknowledgments 266
References 266
Part Three Cell-Matrix and Cell-Cell Crosstalk
14 Crosstalk Between Cell-Cell and Cell-Matrix Adhesion 273
C. Michael DiPenio
14.1 Introduction 273
14.1.1 Coordinate Regulation of Cell-Cell and Cell-Matrix Adhesion 273
14.1.2 Crosstalk Between Integrins and Cadherins 274
14.2 Mechanisms of Integrin-Cadherin Crosstalk 275
14.2.1 Extracellular Proteolysis 275
14.2.2 Cross-Regulation of Gene Expression 277
14.2.3 Changes in Intracellular Force Generation 278
14.2.4 Integrin-Cadherin Associations at Sites of Cell Adhesion 279
14.2.5 Intracellular Signal Transduction Pathways 281
14.2.5.1 FAK: An Integrin Effector that Signals to Cadherins 282
14.2.5.2 Fer: A Tyrosine Kinase that Translocates between Cadherins and
Integrins 282
14.2.5.3 Rapl: A Central Regulator of Integrin-Cadherin Crosstalk
Pathways? 283
14.2.5.4 The Epidermis as a Model for Investigating Cadherin-Integrin
Crosstalk 285
14.3 Future Prospects 286
Acknowledgments 287
References 287
Index 295
Contents XIII
6.2.3 Summary 215
6.2.4 Perspectives 215
6.2.5 Sample Preparation: Short Protocol 215
6.2.5.1 Recommended Equipment and Consumables 215
6.2.5.2 Preparation of the Source Plate 216
6.2.5.3 Spotting 217
6.2.5.4 Cell Culture and Experiment 217
References 218
6.3 Sample Preparation by Laser Microdissection and Catapulting
for Proteome Analysis 219
Karin Schutze, Andrea Buchstaller, Yilmaz Niyaz, Christian Melle,
Gunther Ernst, Kerstin David, Thorsten Schlomm,
and Ferdinand von Eggeling
6.3.1 Introduction: Laser Microdissection and Functional Proteomic
Research 219
6.3.2 The Relevance of Pure Starring Material for Proteomics 219
6.3.3 Examples of Combined LMPC and Proteomic Analyses 220
6.3.3.1 LMPC and Preeclampsia 220
6.3.3.2 LMPC and Renal Cell Carcinoma 221
6.3.3.3 LMPC and Hepatocellular Carcinoma 221
6.3.3.4 LMPC and Brain Disorders 221
6.3.3.5 LMPC and Plant Biology 221
6.3.4 LMPC Adapted for Proteomic Applications 222
6.3.5 LMPC Combined with SELDI-TOF MS: A Promising Approach
for Patient-Specific Analyses 224
6.3.6 Correlation of Gene and Protein Expression: The Best Data
Capture for Comprehensive Diagnosis 228
6.3.7 Recipe for Beginners 228
6.3.7.1 Patients and Specimens 228
6.3.7.2 Laser Microdissection of Tissue Sections 230
6.3.7.3 ProteinChip Array Preparation and Analysis 230
6.3.8 Summary and Outlook 231
References 232
6.4 Sample Preparation for Flow Cytometry 234
Derek C. Davies
6.4.1 Introduction 234
6.4.2 Sample Preparation for Flow Cytometry 236
6.4.2.1 Preparation from Cells in Suspension 236
6.4.2.2 Preparation from Adherent Cells 237
6.4.2.3 Preparation from Solid Tissue 237
6.4.2.4 General Considerations 237
6.4.3 Identification of Relevant Cells 238
6.4.4 Cell Sorting 238
6.4.4.1 Cells and Samples 238
6.4.4.2 Cytometer Considerations 239
XIV Contents
6.4.5 Application Example 240
6.4.6 Summary 242
6.4.7 Perspectives 242
6.4.8 Recipes for Beginners 242
6.4.8.1 Cultured Suspension Cells 242
6.4.8.2 Adherent Cells 242
6.4.8.3 Solid Tissue 243
References 243
7 Chromatography 245
7.1 Sample Preparation for HPLC-Based Proteome Analysis 245
Egidijus Machtejevas and Klaus K. Unger
7.1.1 Introduction 245
7.1.2 Problems Related to Direct Sample Injection in HPLC 246
7.1.3 Trial and Error Selection of the Sample Preparation Method 247
7.1.4 Classical Approaches 249
7.1.5 Specific Approaches Applied to Sample Clean-Up in Proteomics 250
7.1.5.1 Miniaturized Extraction Techniques 250
7.1.5.2 Most Abundant Component Depletion 250
7.1.5.3 Affinity-Enrichment Approaches 251
7.1.6 On-line Sample Clean-Up Approaches 252
7.1.7 Restricted Access Technology 254
7.1.8 Application Example: The Case Study 259
7.1.9 Conclusion and Perspectives 260
References 262
7.2 Sample Preparation for Two-Dimensional Phosphopeptide
Mapping and Phosphoamino Acid Analysis 265
Anamarija Kruljac-Letunic and Andree Blaukat
7.2.1 Introduction 265
7.2.2 Important Aspects in Sample Preparation Procedures 265
7.2.3 Application Example 267
7.2.4 Summary 267
7.2.5 Perspective 269
7.2.6 Recipe for Beginners 269
7.2.6.1 2-D Phosphopeptide Mapping Procedure 269
7.2.6.2 Phosphoamino Acid Analysis Procedure 271
References 271
8 Structural Proteomics 273
8.1 Exploring Protein-Iigand Interactions by Solution NMR 273
Rudolf Hartmann, Thomas Slangier, Bernd W.Konig,
and Dieter Willbold
8.1.1 Introduction 273
8.1.2 Localization of Interaction Sites by Chemical Shift Perturbation
(CSP) Mapping 274
Contents XV
8.1.3 Saturation Transfer Difference Spectroscopy 276
8.1.4 Iigand Screening by NMR 278
References 279
8.2 Sample Preparation for Crystallography 281
Djordje Musil
8.2.1 Introduction 281
8.2.2 Use of Recombinant Proteins in Crystallization 282
8.2.3 Protein Solubility and Crystallization 284
8.2.4 Protein Crystallization 286
8.2.5 Practical Examples 291
References 292
9 Interaction Analysis 295
9.1 Sample Preparation for Protein Complex Analysis by the
Tandem Affinity Purification (TAP) Method 295
Bertrand Siraphin and Andrzej Dziembowski
9.1.1 Introduction 295
9.1.2 The Problem with Regards to Sample Preparation:
The Pros and the Cons 296
9.1.3 Application Example 300
9.1.4 Summary 301
9.1.5 Perspective 301
9.1.6 Recipe for Beginners 301
References 302
9.2 Exploring Membrane Proteomes 303
Filippa Stenberg and Daniel O. Daley
9.2.1 Introduction 303
9.2.2 Defining Membrane Proteomes 303
9.2.3 Separation of Membrane Proteomes 304
9.2.4 Experimental Identification of Membrane Proteins 307
9.2.5 Mapping Membrane Interactomes 307
9.2.6 Structural Analysis of Membrane Proteomes 308
9.2.7 Summary and Perspective 309
9.2.8 Recipe for Beginners 311
9.2.8.1 Sample Preparation 311
9.2.8.2 BN-PAGE 311
9.2.8.3 SDS-PAGE 312
References 312
10 Post-Translational Modifications 317
10.1 Sample Preparation for Phosphoproteome Analysis 317
Rent P. Zahedi and Albert Sickmann
10.1.1 Introduction 317
10.1.2 General Sample Preparation 317
XVI Contents
10.1.3 Reduction of Sample Complexity 318
10.1.3.1 Gel Electrophoresis 318
10.1.3.2 Isoelectric Focusing 318
10.1.4 Methods for Phosphopeptide/Protein Enrichment 319
10.1.4.1 Immunoprecipitation 319
10.1.4.2 Immobilized Metal Ion Affinity Chromatography (IMAC) 319
10.1.4.3 Metal Oxides 320
10.1.4.4 Cation-Exchange Chromatography 321
10.1.4.5 Derivatization Approaches 322
10.1.5 Summary 323
10.1.6 Perspective 324
10.1.7 Recipe for Beginners: IMAC 324
References 325
10.2 Sample Preparation for Analysis of Post-Translarional
Modifications: Glycosylation 328
David S. Selby, Martin R. Larsen, MirenJ. Omaetxebarria,
and Peter Roepstorff
10.2.1 Introduction 328
10.2.2 Advantages and Disadvantages of Different Sample
Preparation Methods 331
10.2.3 Example Applications of Enrichment Methods 334
10.2.3.1 ZIC-HILIC Microcolumns for Preparation of N-Linked
Glycan-Containing Samples 334
10.2.3.2 Titanium Dioxide Microcolumns for Enrichment of Sialic
Acid-Containing Glycopeptides and Glycosylphosphatidylinositol
lipid-Anchored Peptides 336
10.2.4 Summary 337
10.2.5 Perspective 338
10.2.6 Recipe for Beginners: Enrichment of Glycopeptides with a
HILIC Microcolumn 338
10.2.6.1 Materials 338
10.2.6.2 Procedure: Purification of Glycopeptides 339
10.2.6.3 Procedure: Deglycosylation of N-Linked Glycopeptides 339
References 340
11 Species-Dependent Proteomics 343
11.1 Sample Preparation and Data Processing in Plant Proteomics 343
Katja Baerenfaller, Wilhelm Cruissem, and Sacha Baginsky
11.1.1 Introduction 343
11.1.2 Plant-Specific Considerations in Proteomics 344
11.1.2.1 Cell Walls 344
11.1.2.2 Plasrids 344
11.1.2.3 Protein Extraction from Plant Tissue 345
11.1.2.4 Extraction from Recalcitrant and Resistant Tissue 345
Contents XVII
11.1.2.5 Dynamic Range limitations 346
11.1.2.6 Proteomics in As-Yet Unsequenced Organisms 346
11.1.3 Sample Preparation Protocols 347
11.1.3.1 Cell Wall Protein Extraction 348
11.1.3.2 Plastid Isolation 349
11.1.3.3 Protein Extraction with TCA/Acetone 350
11.1.3.4 Phenol Extraction 351
11.1.3.5 Serial Extraction 351
11.1.3.6 Extraction from Recalcitrant and Resistant Tissue 352
11.1.3.7 Extraction and Fractionation with Polyethylene Glycol (PEG) 353
11.1.3.8 Stages Following Protein Extraction 353
11.1.4 MS/MS Data Processing for Unsequenced Organisms 354
11.1.5 Concluding Remarks 355
References 356
11.2 Sample Preparation for MudPIT with Bacterial Protein Samples 358
Ansgar Poetsch and Dirk Wolters
11.2.1 Introduction 358
11.2.2 The MudPIT Technology 359
11.2.3 Membrane Proteins and MudPIT 361
11.2.4 Quantitative MudPIT 363
11.2.5 Limitations of MudPIT 364
11.2.6 Pitfalls of MudPIT 365
11.2.7 Summary 365
11.2.8 Perspective 365
11.2.9 Recipe for Beginners: MudPIT: Soluble and Membrane Proteins 366
References 368
11.3 Sample Preparation for the Cell-Wall Proteome Analysis of Yeast
and Fungi 371
Kai Sohn, Ekkehard Hitler, and Steffen Rupp
11.3.1 Introduction 371
11.3.2 Description of the Problem with Regards to Sample Preparation 372
11.3.3 Application Example 373
11.3.4 Summary 375
11.3.5 Perspective 376
11.3.6 Recipe for Beginners 376
11.3.6.1 Cultures 376
11.3.6.2 Preparation of Soluble Cell-Surface Proteins 376
11.3.6.3 Preparation of Peptides from Covalently Linked Cell-Wall Proteins 377
References 378
12 The Human Proteosome 379
12.1 Clinical Proteomics: Sample Preparation and Standardization 379
Cerd Schmitz and Carsten Gnewuch
12.1.1 Introduction 379
XVIII Contents
12.1.2 The Preanalytical Phase: Sample Preparation, Standardization,
and Quality Management 380
12.1.2.1 Standardization of the (Pre)-Analytical Process 381
12.1.3 Proteomics in Body Fluids 382
12.1.3.1 Techniques for Proteomic Analysis 382
12.1.3.2 Applications 383
12.1.3.3 Preparation of Clinical Samples for Fluidic Proteomics 386
12.1.4 Cellular Proteomics (Cytomics) 389
12.1.4.1 Sample Preparation and Standardization for Clinical Cytomics 389
12.1.4.2 Tissue Arrays 390
12.1.4.3 Bead-Based Immunoassays for Protein Analysis 391
12.1.4.4 Preparative Methods 391
12.1.4.5 Clinical Applications in Cytomics 399
12.1.5 Conclusion 404
References 405
12.2 Stem Cell Proteomics 412
Regina Ebert, Cabriele Miiller, Jerzy Aclamski, and Franz Jakob
12.2.1 Introduction 412
12.2.2 Stem Cell Niches 413
12.2.3 Why Study Proteomes in Stem Cells? 413
12.2.4 Technical Challenges and Problems 414
12.2.4.1 Stem Cell Preparation 414
12.2.4.2 Cultivation 415
12.2.4.3 Treatment 415
12.2.4.4 Whole-Cell Proteome 415
12.2.4.5 Secretory Proteome 415
12.2.5 Recipes for Beginners 417
12.2.5.1 Whole-Cell Lysate 417
12.2.5.2 Secretory Proteome Procedure 418
12.2.5.3 Labeling with 35S 418
12.2.5.4 Ethanol Precipitation 419
12.2.5.5 TCA Precipitation 419
References 419
13 Bioinformatics 423
13.1 Bioinformatics Support for Mass Spectrometric Quality Control 423
Knut Reinert, Tim Conrad, and Oliver Kohlbacher
13.1.1 Introduction 423
13.1.2 Problem description 423
13.1.2.1 Signal Processing Pitfalls 424
13.1.2.2 Map Quality Control 425
13.1.2.3 Statistical Validation Results 425
13.1.3 Quality Assessment for One-Dimensional (1-D) MS Data 426
13.1.3.1 Filter 427
Contents I XIX
13.1.4 Application Example: Absolute Quantification of an Unknown
Peptide Content 428
13.1.5 Summary 429
13.1.6 Perspective 430
13.1.7 Recipe for Beginners 430
13.1.7.1 Acquiring the Raw Data 430
13.1.7.2 Preprocessing the Data 431
13.1.7.3 Analyzing the Preprocessed Data 431
References 431
13.2 Use of Physico-Chemical Properties in Peptide and Protein
Identification 433
Anastasia K. Yocum, PeterJ. Ulintz, and Philip C. Andrews
13.2.1 Introduction 433
13.2.2 Isoelectric Point 434
13.2.3 Ion-Exchange Chromatography 436
13.2.4 Reversed-Phase Chromatography 438
13.2.5 Mass Accuracy 442
13.2.6 Summary 443
References 444
Index 449 |
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| bvnumber | BV023308549 |
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| genre_facet | Aufsatzsammlung |
| id | DE-604.BV023308549 |
| illustrated | Illustrated |
| index_date | 2024-07-02T20:49:25Z |
| indexdate | 2024-07-20T09:40:05Z |
| institution | BVB |
| isbn | 9783527318827 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016492873 |
| oclc_num | 227329702 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-634 DE-11 DE-188 DE-578 |
| owner_facet | DE-355 DE-BY-UBR DE-634 DE-11 DE-188 DE-578 |
| physical | XV, 301 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Wiley-VCH-Verl. |
| record_format | marc |
| spelling | Cell junctions adhesion, development, and disease ed. by Susan E. LaFlamme ... Weinheim Wiley-VCH-Verl. 2008 XV, 301 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Cells cabt Signal Transduction cabt Cytoadherence cabt Gap Junctions cabt Zellkontakt (DE-588)4370909-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Zellkontakt (DE-588)4370909-6 s b DE-604 LaFlamme, Susan E. Sonstige oth text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3008353&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016492873&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Cell junctions adhesion, development, and disease Cells cabt Signal Transduction cabt Cytoadherence cabt Gap Junctions cabt Zellkontakt (DE-588)4370909-6 gnd |
| subject_GND | (DE-588)4370909-6 (DE-588)4143413-4 |
| title | Cell junctions adhesion, development, and disease |
| title_auth | Cell junctions adhesion, development, and disease |
| title_exact_search | Cell junctions adhesion, development, and disease |
| title_exact_search_txtP | Cell junctions adhesion, development, and disease |
| title_full | Cell junctions adhesion, development, and disease ed. by Susan E. LaFlamme ... |
| title_fullStr | Cell junctions adhesion, development, and disease ed. by Susan E. LaFlamme ... |
| title_full_unstemmed | Cell junctions adhesion, development, and disease ed. by Susan E. LaFlamme ... |
| title_short | Cell junctions |
| title_sort | cell junctions adhesion development and disease |
| title_sub | adhesion, development, and disease |
| topic | Cells cabt Signal Transduction cabt Cytoadherence cabt Gap Junctions cabt Zellkontakt (DE-588)4370909-6 gnd |
| topic_facet | Cells Signal Transduction Cytoadherence Gap Junctions Zellkontakt Aufsatzsammlung |
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