Protein aggregation : methods and protocols

著者

• Cieplak, Andrzej

書誌事項

Protein aggregation : methods and protocols

edited by Andrzej Cieplak

（Methods in molecular biology / John M. Walker, series editor, 2551）（Springer protocols）

Humana Press, c2023

注記

Includes bibliographical references and index

内容説明・目次

内容説明

The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Aggregation: Methods and Protocols aims to be useful and practical guide to new researchers and experts looking to expand their knowledge.

目次

1. Early aggregation of Amyloid- (1-42) studied by Fluorescence Correlation Spectroscopy Mercedes Novo, Cibran Perez-Gonzalez, Sonia Freire, and Wajih Al-Soufi 2. Preparation and investigation of crucial oligomers in the early stages of A 40 and A 42 aggregation Bertrand Morel and Francisco Conejero-Lara 3. Preparation and fractionation of heterogeneous A 42 oligomers with different aggregation properties Erica W. Chen and Zhefeng Guo 4. An efficient method of expression and purification of amyloid beta (A 1-42) peptide from E.coli Dhiman Ghosh, Marielle Aulikki Walti, and Roland Riek 5. Solid-state NMR structure of amyloid- fibrils Beat H. Meier and Anja Boeckmann 6. Time-resolved in situ AFM measurement of growth rates of A 40 fibrils Peter G. Vekilov and Peter G. Wolynes 7. Monitoring kinetics of pH-dependent aggregation and disaggregation of the Pmel17 repeat domain Dexter N. Dean and Jennifer C. Lee 8.Analysis of Tau:nucleoporin interactions by Surface Plasmon Resonance Spectroscopy Lisa Diez, Larisa E. Kapinos, Roderick Y. H. Lim, and Susanne Wegmann 9. Microfluidic chamber technology to study missorting and spreading of Tau protein in Alzheimer disease Senthilvelrajan Kaniyappan, Varun Balaji, Yipeng Wang, and Eckhard Mandelkow 10. Using FRET-based biosensor cells to study the seeding activity of tau and -synuclein Katherine N. Maina, Caroline Smet-Nocca, and Gal Bitan 11. Functional applications of stable tau oligomers in cell biology and electrophysiology studies Emily Hill, Kevin G. Moffat, Mark J. Wall, Henrik Zetterberg, Kaj Blennow, and Thomas K. Karikari 12. An additive-free model for tau self-assembly Youssra K Al-Hilaly, Karen E Marshall, Liisa Lutter, Luca Biasetti, Kurtis Mengham, Charles R Harrington, Wei-Feng Xue, Claude M Wischik, and Louise C Serpell 13. Cross-linking mass spectrometry analysis of metastable compact structures in intrinsically disordered proteins Dailu Chen and Lukasz A. Joachimiak 14. A validated method to prepare stable tau oligomers Emily Hill, Kevin G. Moffat, Mark J. Wall, Henrik Zetterberg, Kaj Blennow, and Thomas K. Karikari 15. Light microscopy and dynamic light scattering to study liquid-liquid phase separation of Tau proteins in vitro Janine Hochmair, Christian Exner, Christian Betzel, Eckhard Mandelkow, and Susanne Wegmann 16. Study of tau liquid-liquid phase separation in vitro Solomiia Boyko and Witold K. Surewicz 17. Liquid-Liquid Phase Separation to study the association of proteins in solution Irving Vega and Andrew Umstead 18. Mapping phase diagram of tau-RNA LLPS under live cell coculturing conditions Yanxian Lin, Yann Fichou, Jennifer N. Rauch, Xuemei Zhang, Kenneth S. Kosik, and Songi Han 19. The role of buffers in wild-type HEWL amyloid fibril formation mechanism - a methodological approach Sandi Brudar and Barbara Hribar-Lee 20. Reproducible formation of insulin superstructures: amyloid-like fibrils, spherulites and particulates Camilla Thorlaksen, Martin Busch Neergaard, Minna Groenning, and Vito Fodera 21. CD and solid-state NMR studies of low-order oligomers of transthyretin Anvesh K. R. Dasari and Kwang Hun Lim 22. Identifying biological and biophysical features of different maturation states of -synuclein amyloid fibrils Thomas Skamris, Bente Vestergaard, Kenneth L. Madsen, Annette E. Langkilde, and Vito Fodera 23. Preparation of -synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies Luc Bousset, Ania Alik, Ana Arteni, Anja Boeckmann, Beat H. Meier, and Ronald Melki 24. Propagation of distinct alpha-synuclein strains within human reconstructed neuronal network and associated neuronal dysfunctions Simona Gribaudo, Luc Bousset, Josquin Courte, Ronald Melki, Jean-Michel Peyrin, and Anselme L. Perrier 25. Single-particle analysis of the interaction between molecules and protein aggregated species by Dual-Color Time-Resolved Fluorescence Spectroscopy Pablo Gracia and Nunilo Cremades 26. FRAP & FRET investigation of -synuclein fibrillization via liquid-liquid phase separation in vitro and in HeLa cells Soumik Ray, Nitu Singh, Komal Patel, G. Krishnamoorthy, and Samir K. Maji 27. Spectrally-resolved FRET microscopy of -synuclein phase-separated liquid droplets Jaladhar Mahato, Soumik Ray, Samir K. Maji, and Arindam Chowdhury 28. Combined H-N cross polarization and carbonyl detection NMR spectroscopy allows to record high-resolution, high-sensitivity spectra of alpha-synuclein in bacterial cells Juan M. Lopez 29. Identification of distinct soluble states during fibril formation using multilinear analysis of NMR diffusion data Kristine Steen Jensen, Mathias Nilsson, Mikael Akke, and Anders Malmendal 30. Structural analysis of SOD1 fibrils with mass spectrometry, limited proteolysis and atomic force microscopy (AFM) Bon-Kyung Koo and Julian Whitelegge 31. Biophysical studies of LLPS and aggregation of TDP-43 LCD W. Michael Babinchak and Witold K. Surewicz 32. A spectrophotometric turbidity assay to study Liquid-Liquid Phase Separation of UBQLN2 in vitro Peter Raymond-Smied1, Barrington Bucknor, Yiran Yang2, Tongyin Zheng, and Carlos A. Castaneda 33. An optimized SG detection method: Investigation of UBQLN2 effect on RNA-FUS interaction and SG formation Elizabeth J. Alexander and Jiou Wang 34. Neuronal puncta/aggregate formation by wild-type and mutant UBQLN2 Nathaniel Safren, Lisa M. Sharkey and Sami J. Barmada 35. In vivo analysis of a biomolecular condensate in the nervous system of C. elegans Matthew G. Andrusiak and Yishi Jin 36. FLIM-FRET investigation of heterogeneous huntingtin aggregation in HeLa cells Maria Chiara Lionetti and C.A.M La Porta 37. In vitro characterization of protein:nucleic acid liquid-liquid phase separation by microscopy methods and nanoparticle tracking analysis Mariana J. do Amaral, Yulli M. Passos, Marcius S. Almeida, Anderson S. Pinheiro, and Yraima Cordeiro 38. Cross-seeding assay in the investigation of the amyloid core of prion fibrils Brett K.-Y. Chu, Yu-Sheng Lin, Howard C.-H. Shen, and Rita P.-Y. Chen 39 Mapping the domain structure and aggregation propensity of proteins using a Gateway plasmid vector system Beti Zaharija and Nicholas J. Bradshaw 1. Early aggregation of Amyloid- (1-42) studied by Fluorescence Correlation Spectroscopy Mercedes Novo, Cibran Perez-Gonzalez, Sonia Freire, and Wajih Al-Soufi 2. Preparation and investigation of crucial oligomers in the early stages of A 40 and A 42 aggregation Bertrand Morel and Francisco Conejero-Lara 3. Preparation and fractionation of heterogeneous A 42 oligomers with different aggregation properties Erica W. Chen and Zhefeng Guo 4. An efficient method of expression and purification of amyloid beta (A 1-42) peptide from E.coli Dhiman Ghosh, Marielle Aulikki Walti, and Roland Riek 5. Solid-state NMR structure of amyloid- fibrils Beat H. Meier and Anja Boeckmann 6. Time-resolved in situ AFM measurement of growth rates of A 40 fibrils Peter G. Vekilov and Peter G. Wolynes 7. Monitoring kinetics of pH-dependent aggregation and disaggregation of the Pmel17 repeat domain Dexter N. Dean and Jennifer C. Lee 8.Analysis of Tau:nucleoporin interactions by Surface Plasmon Resonance Spectroscopy Lisa Diez, Larisa E. Kapinos, Roderick Y. H. Lim, and Susanne Wegmann 9. Microfluidic chamber technology to study missorting and spreading of Tau protein in Alzheimer disease Senthilvelrajan Kaniyappan, Varun Balaji, Yipeng Wang, and Eckhard Mandelkow 10. Using FRET-based biosensor cells to study the seeding activity of tau and -synuclein Katherine N. Maina, Caroline Smet-Nocca, and Gal Bitan 11. Functional applications of stable tau oligomers in cell biology and electrophysiology studies Emily Hill, Kevin G. Moffat, Mark J. Wall, Henrik Zetterberg, Kaj Blennow, and Thomas K. Karikari 12. An additive-free model for tau self-assembly Youssra K Al-Hilaly, Karen E Marshall, Liisa Lutter, Luca Biasetti, Kurtis Mengham, Charles R Harrington, Wei-Feng Xue, Claude M Wischik, and Louise C Serpell 13. Cross-linking mass spectrometry analysis of metastable compact structures in intrinsically disordered proteins Dailu Chen and Lukasz A. Joachimiak 14. A validated method to prepare stable tau oligomers Emily Hill, Kevin G. Moffat, Mark J. Wall, Henrik Zetterberg, Kaj Blennow, and Thomas K. Karikari 15. Light microscopy and dynamic light scattering to study liquid-liquid phase separation of Tau proteins in vitro Janine Hochmair, Christian Exner, Christian Betzel, Eckhard Mandelkow, and Susanne Wegmann 16. Study of tau liquid-liquid phase separation in vitro Solomiia Boyko and Witold K. Surewicz 17. Liquid-Liquid Phase Separation to study the association of proteins in solution Irving Vega and Andrew Umstead 18. Mapping phase diagram of tau-RNA LLPS under live cell coculturing conditions Yanxian Lin, Yann Fichou, Jennifer N. Rauch, Xuemei Zhang, Kenneth S. Kosik, and Songi Han 19. The role of buffers in wild-type HEWL amyloid fibril formation mechanism - a methodological approach Sandi Brudar and Barbara Hribar-Lee 20. Reproducible formation of insulin superstructures: amyloid-like fibrils, spherulites and particulates Camilla Thorlaksen, Martin Busch Neergaard, Minna Groenning, and Vito Fodera 21. CD and solid-state NMR studies of low-order oligomers of transthyretin Anvesh K. R. Dasari and Kwang Hun Lim 22. Identifying biological and biophysical features of different maturation states of -synuclein amyloid fibrils Thomas Skamris, Bente Vestergaard, Kenneth L. Madsen, Annette E. Langkilde, and Vito Fodera 23. Preparation of -synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies Luc Bousset, Ania Alik, Ana Arteni, Anja Boeckmann, Beat H. Meier, and Ronald Melki 24. Propagation of distinct alpha-synuclein strains within human reconstructed neuronal network and associated neuronal dysfunctions Simona Gribaudo, Luc Bousset, Josquin Courte, Ronald Melki, Jean-Michel Peyrin, and Anselme L. Perrier 25. Single-particle analysis of the interaction between molecules and protein aggregated species by Dual-Color Time-Resolved Fluorescence Spectroscopy Pablo Gracia and Nunilo Cremades 26. FRAP & FRET investigation of -synuclein fibrillization via liquid-liquid phase separation in vitro and in HeLa cells Soumik Ray, Nitu Singh, Komal Patel, G. Krishnamoorthy, and Samir K. Maji 27. Spectrally-resolved FRET microscopy of -synuclein phase-separated liquid droplets Jaladhar Mahato, Soumik Ray, Samir K. Maji, and Arindam Chowdhury 28. Combined H-N cross polarization and carbonyl detection NMR spectroscopy allows to record high-resolution, high-sensitivity spectra of alpha-synuclein in bacterial cells Juan M. Lopez 29. Identification of distinct soluble states during fibril formation using multilinear analysis of NMR diffusion data Kristine Steen Jensen, Mathias Nilsson, Mikael Akke, and Anders Malmendal 30. Structural analysis of SOD1 fibrils with mass spectrometry, limited proteolysis and atomic force microscopy (AFM) Bon-Kyung Koo and Julian Whitelegge 31. Biophysical studies of LLPS and aggregation of TDP-43 LCD W. Michael Babinchak and Witold K. Surewicz 32. A spectrophotometric turbidity assay to study Liquid-Liquid Phase Separation of UBQLN2 in vitro Peter Raymond-Smied1, Barrington Bucknor, Yiran Yang2, Tongyin Zheng, and Carlos A. Castaneda 33. An optimized SG detection method: Investigation of UBQLN2 effect on RNA-FUS interaction and SG formation Elizabeth J. Alexander and Jiou Wang 34. Neuronal puncta/aggregate formation by wild-type and mutant UBQLN2 Nathaniel Safren, Lisa M. Sharkey and Sami J. Barmada 35. In vivo analysis of a biomolecular condensate in the nervous system of C. elegans Matthew G. Andrusiak and Yishi Jin 36. FLIM-FRET investigation of heterogeneous huntingtin aggregation in HeLa cells Maria Chiara Lionetti and C.A.M La Porta 37. In vitro characterization of protein:nucleic acid liquid-liquid phase separation by microscopy methods and nanoparticle tracking analysis Mariana J. do Amaral, Yulli M. Passos, Marcius S. Almeida, Anderson S. Pinheiro, and Yraima Cordeiro 38. Cross-seeding assay in the investigation of the amyloid core of prion fibrils Brett K.-Y. Chu, Yu-Sheng Lin, Howard C.-H. Shen, and Rita P.-Y. Chen 39 Mapping the domain structure and aggregation propensity of proteins using a Gateway plasmid vector system Beti Zaharija and Nicholas J. Bradshaw

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詳細情報

• NII書誌ID(NCID): BD02885775
• ISBN:
  • 9781071625965
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York
• ページ数/冊数: xvi, 681 p.
• 大きさ: 27 cm
• 分類:
  • DC23 : 572.633
• 件名:
  • LCSH : Protein binding
  • LCSH : Protein folding
  • LCSH : Proteins -- Denaturation
  • LCSH : Cell aggregation
• 親書誌ID:
  • BA10794673
  • BA88873632