Protein Aggregation

ISBN-13: 9781071625996 / Angielski / Miękka / 2023

Opis

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.

Spis treści

1. Early aggregation of Amyloid-β (1-42) studied by Fluorescence Correlation Spectroscopy

Mercedes Novo, Cibrán Pérez-González, Sonia Freire, and Wajih Al-Soufi

 

2. Preparation and investigation of crucial oligomers in the early stages of Aβ40 and Aβ42                 aggregation

Bertrand Morel and Francisco Conejero-Lara

 

3. Preparation and fractionation of heterogeneous Aβ42 oligomers with different aggregation properties

Erica W. Chen and Zhefeng Guo

 

4. An efficient method of expression and purification of amyloid beta (Aβ_1-42) peptide from E.coli

Dhiman Ghosh, Marielle Aulikki Wälti, and Roland Riek

 

5. Solid-state NMR structure of amyloid-β fibrils

Beat H. Meier and Anja Böckmann

 

6. Time-resolved in situ AFM measurement of growth rates of Aβ40 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 α-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 Foderà

 

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 α-synuclein amyloid fibrils

Thomas Skamris, Bente Vestergaard, Kenneth L. Madsen, Annette E. Langkilde, and Vito Foderà

 

23. Preparation of α-synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies

Luc Bousset, Ania Alik, Ana Arteni, Anja Böckmann, 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 α-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. Castañeda

 

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-β (1-42) studied by Fluorescence Correlation Spectroscopy

Mercedes Novo, Cibrán Pérez-González, Sonia Freire, and Wajih Al-Soufi

 

2. Preparation and investigation of crucial oligomers in the early stages of Aβ40 and Aβ42                 aggregation

Bertrand Morel and Francisco Conejero-Lara

 

3. Preparation and fractionation of heterogeneous Aβ42 oligomers with different aggregation properties

Erica W. Chen and Zhefeng Guo

 

4. An efficient method of expression and purification of amyloid beta (Aβ_1-42) peptide from E.coli

Dhiman Ghosh, Marielle Aulikki Wälti, and Roland Riek

 

5. Solid-state NMR structure of amyloid-β fibrils

Beat H. Meier and Anja Böckmann

 

6. Time-resolved in situ AFM measurement of growth rates of Aβ40 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 α-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 Foderà

 

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 α-synuclein amyloid fibrils

Thomas Skamris, Bente Vestergaard, Kenneth L. Madsen, Annette E. Langkilde, and Vito Foderà

 

23. Preparation of α-synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies

Luc Bousset, Ania Alik, Ana Arteni, Anja Böckmann, 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 α-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. Castañeda

 

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