Intermediate filament proteins:
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| Other Authors: | , |
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| Format: | Electronic eBook |
| Language: | English |
| Published: |
Cambridge, MA
Academic Press
2016
|
| Edition: | First edition |
| Series: | Methods in enzymology
volume 568 |
| Subjects: | |
| Online Access: | TUM01 UBM01 UBR01 UBT01 UER01 Volltext Inhaltsverzeichnis |
| Physical Description: | 1 Online-Ressource |
| ISBN: | 9780128034705 9780128034910 |
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Record in the Search Index
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| adam_text | Titel: Intermediate filament proteins
Autor: Omary, M. Bishr
Jahr: 2016
CONTENTS
Contributors xv
Preface xxiii
Acknowledgments xxv
Part I
General Methods to Study IF Proteins
1 - How to Study Intermediate Filaments in Atomic Detail 3
Anastasia A. Chernyatina, John F. Hess, Dmytro Guzenko, John C. Voss,
and Sergei V. Strelkov
1. Introductory Remarks 4
2. Bioinformatics 5
3. X-ray Crystallography 7
4. Electron Paramagnetic Resonance with Site-Directed Spin Labeling 21
5. Concluding Remarks 27
Acknowledgments 28
References 28
2. Mechanical Properties of Intermediate Filament Proteins 35
Elisabeth E. Charrier and Paul A. Janmey
1. Introduction 36
2. Viscoelasticity of Purified IFs In Vitro 36
3. IFs and the Mechanical Properties of Cells 42
4. Conclusion 53
Acknowledgments 54
References 54
3. Multidimensional Monitoring of Keratin Intermediate
Filaments in Cultured Cells and Tissues 59
Nicole Schwarz, Marcin Moch, Reinhard Windoffer, and Rudolf E. Leube
1. Introduction 60
2. 3D Imaging of Keratin Intermediate Filaments in Cultured Cells 62
3. 3D Imaging of Keratin Intermediate Filaments in Murine
Preimplantation Embryos 75
4. Outlook 80
Acknowledgments 81
References 81
vii |
viii Contents
4. Phospho-Specific Antibody Probes of Intermediate
Filament Proteins 85
Hidemasa Goto, Hiroki Tanaka, Kousuke Kasahara, and Masaki Inagaki
1. Introduction 86
2. Production of Site- and Phosphorylation State-Specific Antibodies 91
3. Characterization of Site- and Phosphorylation State-Specific Antibodies 97
4. Immunocytochemistry 100
5. Other Applications 105
6. Conclusions 105
Acknowledgments 106
References 106
5. Assays for Posttranslational Modifications of Intermediate
Filament Proteins 113
Natasha T. Snider and M. Bishr Omary
1. Introduction 114
2. Extraction of IF Proteins from Tissues and Cells for Biochemical
Analysis of IF PTMs 120
3. Methods for Monitoring Specific PTMs on IF Proteins 126
4. Conclusions 135
Acknowledgments 135
References 135
6. Immunofluorescence and Immunohistochemical Detection
of Keratins 139
Cornelia Stumptner, Margit Gogg-Kamerer, Christian Viertler, Helmut Denk,
and Kurt Zatloukal
1. Introduction
2. Impact of Molecular Structure on the Detection of Keratins
in Frozen Tissue Samples
3. Keratin Immunohistochemistry on Paraffin-Embedded Tissue
4. Conclusions
5. Pearls and Pitfalls
Acknowledgments
References
7. High-Throughput Screening for Drugs that Modulate
Intermediate Filament Proteins
Jingyuan Sun, Vincent E. Groppi, Honglian Gui, Lu Chen, Qing Xie, Li Liu,
and M. Bishr Omary
1. Overview of Intermediate Filaments and Their Associated Diseases 164
2. Current Targeted Therapeutic Approaches for IF-Pathies 165
140
142
146
159
159
160
160
163
Contents
ix
3. Unbiased Drug Screening to Target IF Mutations 170
4. High-Throughput Steps to Identify Drugs that Target
Intermediate Filaments 171
5. Available Libraries and Vendors for Drug Screening 179
6. Pearls and Pitfalls 182
Acknowledgments 183
References 183
8. The Use of Withaferin A to Study Intermediate Filaments 187
Royce Mohan and Paola Bargagna-Mohan
1. Introduction 188
2. WFA: A Novel Chemical Tool for IF Biology and Pharmacology 194
3. Targeting IFs 197
4. Primary Cell Culture Systems 207
5. Ocular Injury Model of Fibrosis 209
6. Techniques 211
7. Perspectives 213
Acknowledgments 214
References 214
9. Assays to Study Consequences of Cytoplasmic
Intermediate Filament Mutations: The Case of
Epidermal Keratins 219
Tong San Tan, Yi Zhen Ng, Cedric Badowski, Tram Dang, John E.A. Common,
Lukas Lacina, lldikd SzeverSnyi, and E. Birgitte Lane
1. Introduction 221
2. Identification of Keratin Mutations 223
3. Developing Experimental Model Systems 227
4. Keratin Mutations in Stress Assays 238
5. Conclusion, Pearls, and Pitfalls 246
Acknowledgments 248
References 248
10. Using Data Mining and Computational Approaches to Study
Intermediate Filament Structure and Function 255
David A.D. Parry
1. Introduction 256
2. Methodology 259
3. Summary 270
References 273
X
Contents
Part II
Mammalian IF Proteins
11. Isolation and Analysis of Keratins and Keratin-Associated
Proteins from Hair and Wool 279
Santanu Deb-Choudhury, Jeffrey E. Plowman, and Duane P. Harland
1. Introduction 280
2. Chemical Extraction of Whole Fibers 281
3. Isolation and Digestion of Other Components of the Fiber 286
4. Combination of Sodium Deoxycholate and C18 Empore™ for an Efficient
Extraction of Keratin Peptides from Gel-Resolved Keratin Proteins 290
5. Ionic Liquid-Assisted Extraction of Fiber Keratins 294
6. Conclusions 299
References 300
12. Skin Keratins 303
Fengrong Wang, Abigail Zieman, and Pierre A. Coulombe
1. Introduction 305
2. Collection of Mouse Skin Tissue for Analysis 311
3. Cell Culture Studies 319
4. in Vitro Methods to Study Keratin Proteins 330
5. Pearls and Pitfalls 337
6. Conclusions 340
Acknowledgments 340
Appendix 340
References 346
13. Simple Epithelial Keratins 351
Pavel Strnad, Nurdan Guldiken, Terhi O. Helenius, Julia O. Misiorek,
Joel H. Nystrom, Iris A.K. Lahdeniemi, Jonas S.G. Silvander, Deniz Kuscuoglu,
and Diana M. Toivola
1. Introduction 352
2. Isolation of SEKs 354
3. Studying SEKs in Cell Culture 357
4. Genetic Mouse Models of SEKs 365
5. MDBs—Keratin Aggregates in Liver Disease 372
6. SEK Variant Detection in Humans 378
7. Conclusions 379
Acknowledgments 380
References 380
Contents
xi
14. Methods for Determining the Cellular Functions of Vimentin
Intermediate Filaments 389
Karen M. Ridge, Dale Shumaker, Amelie Robert, Caroline Hookway,
Vladimir I. Gelfand, Paul A. Janmey, Jason Lowery, Ming Guo,
David A. Weitz, Edward Kuczmarski, and Robert D. Goldman
1. Introduction 391
2. Disruption of Vimentin IFs 391
3. Analysis of Vimentin Dynamics Using Photoactivatable and
Photoconvertible Protein Tags 398
4. Investigating Vimentin-Protein Interactions 405
5. Investigating the Mechanical Properties of Vimentin IF Networks 411
6. Investigating the Role of Vimentin IFs in Cell Mechanics 415
7. Conclusion 420
Acknowledgments 421
References 421
15. Strategies to Study Desmin in Cardiac Muscle and
Culture Systems 427
Antigoni Diokmetzidou, Mary Tsikitis, Sofia Nikouli, Ismini Kloukina,
Elsa Tsoupri, Stamatis Papathanasiou, Stelios Psarras, Manolis Mavroidis,
and Yassemi Capetanaki
1. Introduction: Desmin s Scaffold—The Fine-Tuning Machinery
of Striated Muscle 428
2. Cell Systems Used for Desmin Studies 430
3. Methods for Desmin Detection (Expression and Localization) 440
4. Methods for Desmin Isolation and Assembly 447
5. Model Animals for Desmin Mutation Studies 451
6. Identification of Desmin-Associated Proteins 452
7. Pearls and Pitfalls 454
References 454
16. Genetic Manipulation of Neurofilament Protein
Phosphorylation 461
Maria R. Jones, Eric Villalbn, and Michael L. Garcia
1. Introduction 462
2. Genetic Manipulation of Mice 464
3. Steps for Creating a Gene-Targeted Mutant of a Mouse 465
4. Conclusions and Applications 471
References 473
xii
Contents
17.a-lntemexin and Peripherin: Expression, Assembly,
Functions, and Roles in Disease 477
Jian Zhao and Ronald K.H. Liem
1. a-lnternexin 478
2. Peripherin 489
3. Conclusion 497
References 498
18. Studying Nestin and its Interrelationship with Cdk5 509
Julia Lindqvist, Num Wistbacka, and John E. Eriksson
1. Introduction 510
2. Cellular Techniques to Study Nestin Functions in Cells 520
3. In Vivo Mouse Models to Study Nestin Function 528
4. Conclusions 530
Acknowledgments 530
References 530
19.Synemin: Molecular Features and the Use of Proximity
Ligation Assay to Study Its Interactions 537
Madhumita Paul and Omar Skalli
1. Synemin 538
2. Reagents and Tools to Study Synemin 545
3. PLA for In Situ Detection of Synemin Interaction with Binding Partners 546
4. Conclusions 552
References 552
20. Targeting Mitogen-Activated Protein Kinase Signaling
in Mouse Models of Cardiomyopathy Caused by Lamin A/C
Gene Mutations 557
Antoine Muchir and Howard J. Worman
1. Introduction 558
2. Mouse Models of Cardiomyopathy Caused by LMNA Mutations 560
3. Altered MAP Kinase Signaling in Hearts of LmnaH222P/H222P Mice 563
4. MAP Kinase Inhibitor Treatment Studies in LmnaH222P/H222P Mice 568
5. Assessment of LmnaH222P/h222P Mice After Treatment with MAP
Kinase Inhibitors 570
6. Conclusions 575
Acknowledgments 577
References 577
Contents xiii
21. In vivo, Ex Vivo, and In Vitro Approaches to Study Intermediate
Filaments in the Eye Lens 581
Miguel Jarrin, Laura Young, Weiju Wu, John M. Girkin, and Roy A. Quinlan
1. Introduction 582
2. Models to Study IFs in the Eye Lens 586
3. Methods to Study IFs 594
4. Concluding Remarks 603
References 603
Part III
Non-Mammalian IF Protein Systems
22. Compartment-Specific Phosphorylation of Squid
Neurofilaments
Philip Grant and Harish C. Pant
1. Introduction
2. Squid Giant Fiber System
3. Isolation of Axoplasm
4. Squid NF Genes
5. Squid NF Antibodies
6. Developmental Regulation of NF Expression
7. NF-Associated Protein Kinases
8. Squid NFs Are Included in Compartment-Specific Multimeric Protein
Complexes: P13suc1 Affinity Chromatography
References
23. Using Xenopus Embryos to Study Transcriptional and
Posttranscriptional Gene Regulatory Mechanisms of
Intermediate Filaments 635
Chen Wang and Ben G. Szaro
1. Introduction 636
2. Preparation of Expression Plasmids 641
3. Microinjection of Xenopus Embryos 644
4. Assays for Gene Expression 649
5. Assays for Effects of as-Regulatory Elements on RNA Processing,
Trafficking, and Translation 651
6. Conclusions 654
Acknowledgments 654
References 654
615
616
617
619
621
622
622
627
628
630
xiv
Contents
24. Intermediate Filaments in Caenorhabditis elegans 661
Noam Zuela and Yosef Gruenbaum
1. Introduction 662
2. Essential Roles of Cytoplasmic IFs in C. elegans 662
3. Essential Roles of Lamin in C. elegans 663
4. Assembly of C. elegans Lamins 668
5. Assembly of C. elegans IFs 670
6. Methods 670
7. Summary 676
Acknowledgments 677
References 677
25. Mechanical Probing of the Intermediate Filament-Rich
Caenorhabditis Elegans Intestine 681
Oliver Jahnel, Bernd Hoffmann, Rudolf Merkel, Olaf Bossinger,
and Rudolf E. Leube
1. Introduction 682
2. Imaging of Intermediate Filaments in C. elegans Intestines
by Epifluorescence Microscopy 686
3. Outline of Intestinal Rings in C. elegans by a Fluorescent Apical
Junction Reporter 688
4. Dissection of Intestines and Vitality Testing 691
5. Experimental Setup for Micropipette Measurements 695
6. Outlook 702
Acknowledgments 703
References 703
26. Using Drosophila for Studies of Intermediate Filaments 707
Jens Bohnekamp, Diane E. Cryderman, Dylan A. Thiemann,
Thomas M. Magin, and Lori L, Wallrath
1. Introduction 708
2. Methods 711
3. Conclusions 723
References 723
Author Index J27
Subject Index 775
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Intermediate filament proteins edited by M. Bishr Omary and Ronald K.H. Liem First edition Cambridge, MA Academic Press 2016 1 Online-Ressource txt rdacontent c rdamedia cr rdacarrier Methods in enzymology volume 568 Proteine (DE-588)4076388-2 gnd rswk-swf Intermediärfilament (DE-588)4162026-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Intermediärfilament (DE-588)4162026-4 s Proteine (DE-588)4076388-2 s b DE-604 Omary, M. Bishr edt Liem, Ronald K. H. edt Methods in enzymology volume 568 (DE-604)BV021328877 568 http://www.sciencedirect.com/science/journal/00766879/568 Verlag URL des Erstveröffentlichers Volltext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028716718&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Intermediate filament proteins Methods in enzymology Proteine (DE-588)4076388-2 gnd Intermediärfilament (DE-588)4162026-4 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4162026-4 (DE-588)4143413-4 |
| title | Intermediate filament proteins |
| title_auth | Intermediate filament proteins |
| title_exact_search | Intermediate filament proteins |
| title_full | Intermediate filament proteins edited by M. Bishr Omary and Ronald K.H. Liem |
| title_fullStr | Intermediate filament proteins edited by M. Bishr Omary and Ronald K.H. Liem |
| title_full_unstemmed | Intermediate filament proteins edited by M. Bishr Omary and Ronald K.H. Liem |
| title_short | Intermediate filament proteins |
| title_sort | intermediate filament proteins |
| topic | Proteine (DE-588)4076388-2 gnd Intermediärfilament (DE-588)4162026-4 gnd |
| topic_facet | Proteine Intermediärfilament Aufsatzsammlung |
| url | http://www.sciencedirect.com/science/journal/00766879/568 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028716718&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV021328877 |
| work_keys_str_mv | AT omarymbishr intermediatefilamentproteins AT liemronaldkh intermediatefilamentproteins |