Biomolecular interactions: Part B
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge, MA ; San Diego, CA
Academic Press, an imprint of Elsevier
2022
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| Ausgabe: | First edition |
| Schriftenreihe: | Methods in cell biology
volume 169 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xvii, 346 Seiten Illustrationen, Diagramme |
| ISBN: | 9780128233535 |
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| adam_text | Contents Contributors................................................................................................................... xi Preface........................................................................................................................ xvii Emerging mechanisms of targeted protein degradation by molecular glues........... 1 CHAPTER 1 Geordon A. Frere, Elvin D. de Araujo, and Patrick T. Gunning Introduction........................................................................................2 Immunomodulatory imide drugs (IMiDs)...................................... 4 3. Splicing inhibitor sulfonamides (SPLAMs)................................... 8 4. CDK12/13:DDB1 glues trigger cyclin К degradation.................. 9 5. BCL6 glues induce polymerization and degradation ofBCL6............................................................................................. 11 6. Methods for measuring protein degradation................................. 13 7. Bridging the gap from “serendegrity” to systematic screening............................................................................................ 15 8. Protein degrader discovery by comparative drug profiling in hyponeddylated cell lines....... .................................................... 15 9. Leveraging cell fate control elements for positive selection of protein degraders.......................................................................... 17 10. Conclusions...................................................................................... 19
References.............................................. 19 1. 2. CHAPTER 2 Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy..................... 27 Uchechukwu Agwuegbo and Kim Carol Jonas 1. Introduction....................................................................................... 28 2. Materials............................................................................................ 30 3. A step-by-step guide toPD-PALM imaging and analysis........... 31 4. Future directions............................................. Acknowledgments.............................. References............................. 37 37 37 V
vi Contents CHAPTER 3 Interaction of alpha-synuclein with lipids................. 43 Neha Kachappilly, Jyotirmay Srivastava, Bani Prasad Swain, and Poonam Thakur 1. Introduction...................................................................................... 44 2. Interaction of a-syn with lipid membranes................................... 49 3. Factors modulating a-syn membrane binding............................... 52 4. a-syn interaction with specific membranes and membrane regions..................................................................................... „..56 Membrane remodelingby a-syn..................................................... 58 6. Conclusion....................................................................................... 59 References........ ......................................................................................59 5. CHAPTER 4 Gel-electrophoresis based method for biomolecularinteraction......................... 67 Tsutomu Arakawa, Masataka Nakagawa, Yui Tomioka, Chiaki Sakuma, Cynthia Li, Tomomi Sato, Ryo Sato, Takashi Shibata, Yasunori Kurosawa, and Teruo Akuta 1. Introduction....................................................................................... 68 2. Difference between SDS-PAGÈ, BN-PAGE and native gel electrophoresis............................................................................. 69 3. Materials...................................... 71 4. Methods................................................ 73 5.
Examples..................................................................................... 82 6. Concludingremarks........................................... 93 7. Notes.................................................................................................. 93 References............................................................................................... 94 * CHAPTER 5 Yeast 2-hybrid assay for investigating the interaction between the centrosome proteins PLK4 and STIL......................................... 97 Harshita Kaséra, Sushil Kumar, and Priyanka Singh 1. Introduction....................................................................................... 98 2. Material............................................................................................ 101 3. Protocol............................................................................................ 103 4. Results................................................... .......................................... 105 5. Discussion........................................................................................ 107 6. Troubleshooting.............................................................................. 110 Acknowledgments................................................................................ Ill Author contributions............................................................................ Ill Conflict of interest................................................................................ Ill
References............................................................................................. Ill
Contents CHAPTER 6 Preparation of a stable CCL5 CCR5 G¡ signaling complex for Cryo-EM analysis............ 115 Polina Isaikina, Ching-Ju Tsai, Ivana Petrovic, Marco Rogowski, Alexandra Meng Dürr, and Stephan Grzesiek 1. Introduction.................................................................................... 116 2. Methods.......................................................................................... 119 3. Discussion and conclusion................................ ............................ 135 Acknowledgments................................................................................ 137 Conflict of interest............................................................................... 137 References.............................................................................................137 CHAPTER 7 Protein engineering and design in ion channels and receptors......................................... 143 Nadira Khatoon, Sushanth Adusumilli, Poulomi Dey, Rachita Sharma, Pradeepti Kampani, Jayasha Shandilya, and Tapan K. Nayak Introduction.................................................................................... 144 Materials................................ 146 3. Methods.......................................................................................... 149 4. Receptor engineering and design................................................. 160 5. Concluding remarks...................................................................... 165 References................................................................................ 165
1. 2. CHAPTER 8 Discovery of Virus-Host interactions using bioinformatic tools............................... 169 Catarina Marques-Pereira, Manuel Pires, and Irina S. Moreira 1. Introduction to Virus-Host interactions........................................ 170 2. Virus-Host databases...................................................................... 172 3. Onnes data....................................................................................... 177 4. Artificial intelligence approaches................................................. 180 5. Virus-Host interaction network approaches................................. 183 6. Virus-Host interaction structural prediction.................................186 7. Conclusions..................... 189 Funding................................................................................................ 189 References............................................................................................189 vii
viii Contents CHAPTER 9 Best practices for resilientautomation of biomolecular simulations............................................ 199 Thomas T. Joseph 1. Introduction..................................................................................... 200 2. Common problems and approaches tosolving them................... 200 3. Conclusion.......................................................................................207 4. Script to generate next equilibrium MD simulation: “Next_namd_prod.py”................................................................... 207 5. Script to facilitate automated resilient FEP calculations using NAMD...................................................................................209 6. Sample analysis script................................................................. 217 References............................................................................................. 218 CHAPTER 10 Label-free impedance measurements to unravel biomolecular interactions involved in G proteincoupled receptor signaling................. 221 Michael Skiba, Judith A. Stolwijk, and Joachim Wegener 1. Introduction..................................................................................... 222 2. Electrochemical impedance measurements to study ligand-receptor interactions.................... 225 3. Agonist and antagonist assays..................... 227 4. Dose-response studies.... ............................................................... 229 5. In-depth analysis of the signal transduction pathway......... ...... 231 6. Receptor
desensitization................................................................ 232 7. Further experimental options and current developments........... 233 Acknowledgments................................................................................ 234 References............................................................................................. 234 CHAPTER 11 Proximity labeling for investigating protein-protein interactions................ 237 Conrad T. Pfeiffer, Joao A. Paulo, Steven P. Gygi, and Howard A. Rockman 1. Introduction.............................................. 238 2. Nonproximity labeling based methods for studying protein-protein interactions...................................................... 239 3. Proximity labeling methods for studying protein-protein interactions...................................................................................... 242 4. Coupling mass spectrometry to proximity labeling.................... 253 5. Advantages and disadvantages of the different methods........... 255 6. Summary..........................................................................................257 Disclosures............................................................................................ 258 References............................................................................................. 258
Contents CHAPTER 12 An intrabody sensor to monitor conformational activation of ß-arrestins.................. 267 Hemlata Dwivedi-Agnihotri, Parishmita Sarma, S. Deeksha, Kouki Kawakami, Asuka Inoue, and Arun K. Shukla 1. Introduction..................................................................................... 268 2. Materials..........................................................................................270 3. Methods............................................................... 271 4. Concluding remarks....................................................................... 275 Acknowledgment................................................................................ 276 References........................................................................................... 276 CHAPTER 13 Nanoluciferase-based methods to monitor activation, modulation and trafficking of atypical chemokine receptors....................... 279 Rafael Luís, Giulia D’Uonnolo, Christie B. Palmer, Max Meyrath, Tomasz Uchański, May Wantz, Bernard Rogister, Bassam Janji, Andy Chevigné, and Martyna Szpakowska 1. 2. 3. 4. 5. 6. Introduction............................ 280 Materials.................... 282 Methods........................................................................................... 285 Controls and additional considerations........................................ 288 Concluding remarks....................... 288 Notes................................................................................................ 291
Acknowledgments................................................................................ 292 References.............................................................................................292 CHAPTER 14 ln-cellulo chemical cross-linking to visualize protein-protein interactions.............. 295 Shirsha Saha, Ashutosh Ranjan, Monika Godara, and Arun K. Shukla 1. Introduction.................................................... 296 2. Materials and methods................................................................... 298 3. Troubleshooting.................................................................... 304 4. Additional considerations.............................................................. 305 5. Concluding remarks........................................................................305 Acknowledgment................................................................................. 305 References............................................................................................ 306 ix
x Contents CHAPTER 15 Nanoluciferase-based complementation assay for systematic profiling of GPCR-GRK interactions...309 Christie B. Palmer, Giulia D’Uonnolo, Rafael Luís, Max Meyrath, Tomasz Uchański, Andy Chevigné, and Martyna Szpakowska 1. Introduction..................................................................................... 310 2. Materials.......................................................................... 313 3. Methods........................................................................................... 316 4. Notes................................................................................................ 317 Acknowledgments............................................................................... 319 References....... ..................................................................................... 319 CHAPTER 16 DNA hydrogels: Principles, synthesis, characterization and applications to cell biology...323 Ankur Singh and Dhiraj Bhatia 1. Introduction..................................................... 324 2. Principle...........................................................................................325 3. Synthesis methods.......................................................................... 325 4. Characterization............................................................................. .329 5. Applications.................................................................................... 333 6. Conclusions and future directions............... ................................. 343
Acknowledgments................................................................................ 344 References......................................................................................:..... 344 *
|
| adam_txt |
Contents Contributors. xi Preface. xvii Emerging mechanisms of targeted protein degradation by molecular glues. 1 CHAPTER 1 Geordon A. Frere, Elvin D. de Araujo, and Patrick T. Gunning Introduction.2 Immunomodulatory imide drugs (IMiDs). 4 3. Splicing inhibitor sulfonamides (SPLAMs). 8 4. CDK12/13:DDB1 glues trigger cyclin К degradation. 9 5. BCL6 glues induce polymerization and degradation ofBCL6. 11 6. Methods for measuring protein degradation. 13 7. Bridging the gap from “serendegrity” to systematic screening. 15 8. Protein degrader discovery by comparative drug profiling in hyponeddylated cell lines. . 15 9. Leveraging cell fate control elements for positive selection of protein degraders. 17 10. Conclusions. 19
References. 19 1. 2. CHAPTER 2 Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy. 27 Uchechukwu Agwuegbo and Kim Carol Jonas 1. Introduction. 28 2. Materials. 30 3. A step-by-step guide toPD-PALM imaging and analysis. 31 4. Future directions. Acknowledgments. References. 37 37 37 V
vi Contents CHAPTER 3 Interaction of alpha-synuclein with lipids. 43 Neha Kachappilly, Jyotirmay Srivastava, Bani Prasad Swain, and Poonam Thakur 1. Introduction. 44 2. Interaction of a-syn with lipid membranes. 49 3. Factors modulating a-syn membrane binding. 52 4. a-syn interaction with specific membranes and membrane regions. „.56 Membrane remodelingby a-syn. 58 6. Conclusion. 59 References. .59 5. CHAPTER 4 Gel-electrophoresis based method for biomolecularinteraction. 67 Tsutomu Arakawa, Masataka Nakagawa, Yui Tomioka, Chiaki Sakuma, Cynthia Li, Tomomi Sato, Ryo Sato, Takashi Shibata, Yasunori Kurosawa, and Teruo Akuta 1. Introduction. 68 2. Difference between SDS-PAGÈ, BN-PAGE and native gel electrophoresis. 69 3. Materials. 71 4. Methods. 73 5.
Examples. 82 6. Concludingremarks. 93 7. Notes. 93 References. 94 * CHAPTER 5 Yeast 2-hybrid assay for investigating the interaction between the centrosome proteins PLK4 and STIL. 97 Harshita Kaséra, Sushil Kumar, and Priyanka Singh 1. Introduction. 98 2. Material. 101 3. Protocol. 103 4. Results. . 105 5. Discussion. 107 6. Troubleshooting. 110 Acknowledgments. Ill Author contributions. Ill Conflict of interest. Ill
References. Ill
Contents CHAPTER 6 Preparation of a stable CCL5 CCR5 G¡ signaling complex for Cryo-EM analysis. 115 Polina Isaikina, Ching-Ju Tsai, Ivana Petrovic, Marco Rogowski, Alexandra Meng Dürr, and Stephan Grzesiek 1. Introduction. 116 2. Methods. 119 3. Discussion and conclusion. . 135 Acknowledgments. 137 Conflict of interest. 137 References.137 CHAPTER 7 Protein engineering and design in ion channels and receptors. 143 Nadira Khatoon, Sushanth Adusumilli, Poulomi Dey, Rachita Sharma, Pradeepti Kampani, Jayasha Shandilya, and Tapan K. Nayak Introduction. 144 Materials. 146 3. Methods. 149 4. Receptor engineering and design. 160 5. Concluding remarks. 165 References. 165
1. 2. CHAPTER 8 Discovery of Virus-Host interactions using bioinformatic tools. 169 Catarina Marques-Pereira, Manuel Pires, and Irina S. Moreira 1. Introduction to Virus-Host interactions. 170 2. Virus-Host databases. 172 3. Onnes data. 177 4. Artificial intelligence approaches. 180 5. Virus-Host interaction network approaches. 183 6. Virus-Host interaction structural prediction.186 7. Conclusions. 189 Funding. 189 References.189 vii
viii Contents CHAPTER 9 Best practices for resilientautomation of biomolecular simulations. 199 Thomas T. Joseph 1. Introduction. 200 2. Common problems and approaches tosolving them. 200 3. Conclusion.207 4. Script to generate next equilibrium MD simulation: “Next_namd_prod.py”. 207 5. Script to facilitate automated resilient FEP calculations using NAMD.209 6. Sample analysis script. 217 References. 218 CHAPTER 10 Label-free impedance measurements to unravel biomolecular interactions involved in G proteincoupled receptor signaling. 221 Michael Skiba, Judith A. Stolwijk, and Joachim Wegener 1. Introduction. 222 2. Electrochemical impedance measurements to study ligand-receptor interactions. 225 3. Agonist and antagonist assays. 227 4. Dose-response studies. . 229 5. In-depth analysis of the signal transduction pathway. . 231 6. Receptor
desensitization. 232 7. Further experimental options and current developments. 233 Acknowledgments. 234 References. 234 CHAPTER 11 Proximity labeling for investigating protein-protein interactions. 237 Conrad T. Pfeiffer, Joao A. Paulo, Steven P. Gygi, and Howard A. Rockman 1. Introduction. 238 2. Nonproximity labeling based methods for studying protein-protein interactions. 239 3. Proximity labeling methods for studying protein-protein interactions. 242 4. Coupling mass spectrometry to proximity labeling. 253 5. Advantages and disadvantages of the different methods. 255 6. Summary.257 Disclosures. 258 References. 258
Contents CHAPTER 12 An intrabody sensor to monitor conformational activation of ß-arrestins. 267 Hemlata Dwivedi-Agnihotri, Parishmita Sarma, S. Deeksha, Kouki Kawakami, Asuka Inoue, and Arun K. Shukla 1. Introduction. 268 2. Materials.270 3. Methods. 271 4. Concluding remarks. 275 Acknowledgment. 276 References. 276 CHAPTER 13 Nanoluciferase-based methods to monitor activation, modulation and trafficking of atypical chemokine receptors. 279 Rafael Luís, Giulia D’Uonnolo, Christie B. Palmer, Max Meyrath, Tomasz Uchański, May Wantz, Bernard Rogister, Bassam Janji, Andy Chevigné, and Martyna Szpakowska 1. 2. 3. 4. 5. 6. Introduction. 280 Materials. 282 Methods. 285 Controls and additional considerations. 288 Concluding remarks. 288 Notes. 291
Acknowledgments. 292 References.292 CHAPTER 14 ln-cellulo chemical cross-linking to visualize protein-protein interactions. 295 Shirsha Saha, Ashutosh Ranjan, Monika Godara, and Arun K. Shukla 1. Introduction. 296 2. Materials and methods. 298 3. Troubleshooting. 304 4. Additional considerations. 305 5. Concluding remarks.305 Acknowledgment. 305 References. 306 ix
x Contents CHAPTER 15 Nanoluciferase-based complementation assay for systematic profiling of GPCR-GRK interactions.309 Christie B. Palmer, Giulia D’Uonnolo, Rafael Luís, Max Meyrath, Tomasz Uchański, Andy Chevigné, and Martyna Szpakowska 1. Introduction. 310 2. Materials. 313 3. Methods. 316 4. Notes. 317 Acknowledgments. 319 References. . 319 CHAPTER 16 DNA hydrogels: Principles, synthesis, characterization and applications to cell biology.323 Ankur Singh and Dhiraj Bhatia 1. Introduction. 324 2. Principle.325 3. Synthesis methods. 325 4. Characterization. .329 5. Applications. 333 6. Conclusions and future directions. . 343
Acknowledgments. 344 References.:. 344 * |
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| spelling | Biomolecular interactions Part B edited by Arun K. Shukla (Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India) First edition Cambridge, MA ; San Diego, CA Academic Press, an imprint of Elsevier 2022 xvii, 346 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Methods in cell biology volume 169 Methods in cell biology (DE-588)4143413-4 Aufsatzsammlung gnd-content Shukla, Arun K. 1981- (DE-588)131837397 edt (DE-604)BV047665583 B Methods in cell biology volume 169 (DE-604)BV002534878 169 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033697500&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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