Intrinsically Disordered Proteins (eBook, PDF)

Methods and Protocols
Redaktion: Kragelund, Birthe B.; Skriver, Karen

• Format: PDF

Produktbeschreibung

The edition details methods to study intrinsically disordered proteins (IDPs) including recent topics such as extremely high-affinity disordered complexes, kinetics that evade established concepts, liquid-liquid phase separation, and novel disorder-driven allosteric mechanisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Intrinsically Disordered Proteins: Methods and Protocols aims to help scientists with different backgrounds to further their investigations into these fascinating and dynamic molecules.

Chapter 24 is available open access under a CC BY 4.0 license via link.springer.com.

Chapters "40 and 42 " are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

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Produktdetails

• Verlag: Springer US
• Seitenzahl: 951
• Erscheinungstermin: 21. Juli 2020
• Englisch
• ISBN-13: 9781071605240
• Artikelnr.: 64700786

Inhaltsangabe

Part I: Sequence Properties

1. Disorder for Dummies: Functional Mutagenesis of Transient Helical Segments in Disordered Proteins

Gary W. Daughdrill

2. Computational Prediction of Intrinsic Disorder in Protein Sequences with the disCoP Meta-predictor

Christopher J. Oldfield, Xiao Fan, Chen Wang, A. Keith Dunker^, and Lukasz Kurgan

3. Computational Prediction of Disordered Protein Motifs using SLiMSuite

Richard J Edwards, Kirsti Paulsen, Carla M Aguilar Gomez, and Åsa Pérez-Bercoff

4. How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource

Marc Gouw, Jesús AlvaradoValverde, Jelena Calyseva, Francesca Diella, Manjeet Kumar, Sushama Michael, Kim Van Roey, Holger Dinkel, and Toby J. Gibson

5. Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER

Garrett M. Ginell and Alex S. Holehouse



6. Exploring Protein Intrinsic Disorder with MobiDB

Alexander Miguel Monzon, András Hatos, Marco Necci, Damiano Piovesan, and Silvio C. E. Tosatto



Part II: Evolution

7. An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins
Janelle Nunez-Castilla and Jessica Siltberg-Liberles



Part III: Production

8. Expression and Purification of an Intrinsically Disordered Protein

Karamjeet K. Singh and Steffen P. Graether

9. Production of Intrinsically Disordered Proteins for Biophysical Studies; Tips and Tricks

Christian Parsbæk Pedersen, Pernille Seiffert, Inna Brakti, and Katrine Bugge

10. Recombinant Production of Monomeric Isotope-Enriched Aggregation-Prone Peptides: Polyglutamine Tracts and Beyond

Albert Escobedo, Giulio Chiesa, and Xavier Salvatella



11. Cell-free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy

Linnéa Isaksson and Anders Pedersen



Part IV: Dynamics, Ensembles, and Structures

12. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-ray Scattering

Amin Sagar, Dmitri Svergun, and Pau Bernadó

13. Determining Rg of IDPs from SAXS data
Ellen Rieloff and Marie Skepö

14. Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements

Sarah Leeb and Jens Danielsson

15. Quantitative Protein Disorder Assessment using NMR Chemical Shifts

Jakob T. Nielsen and Frans A. A. Mulder

16. Determination of pK_a Values in Intrinsically Disordered Proteins

Brandon Payliss and Anthony Mittermaier

17. Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates

Rupashree Dass and Frans A.A. Mulder



Part V: Ensembles by Computation

18. Predicting Conformational Properties of Intrinsically Disordered Proteins from Sequence

Kiersten M. Ruff

19. Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins

Matteo Masetti, Mattia Bernetti, and Andrea Cavalli



20. Computational Protocol for Determining Conformational Ensembles of Intrinsically Disordered Proteins

Robert B. Best

21. Computing, Analyzing and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins

Mustapha Carab Ahmed, Ramon Crehuet, and Kresten Lindorff-Larsen

Part VI: Determinants of Interactions

22. Binding Thermodynamics to Intrinsically Disordered Protein Domains

Arne Schön and Ernesto Freire

23. Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements

Samuel Sparks, Ryo Hayama, Michael P. Rout, and David Cowburn

24. NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions

Christopher A. Waudby and John Christodoulou



25. Measuring Effective Concentrations Enforced by Intrinsically Disordered Linkers

Charlotte S. Sørensen and Magnus Kjaergaard

26. Determining the Protective Activity of IDPs under Partial Dehydration and Freeze-thaw Conditions

David F. Rendón-Luna, Paulette S. Romero-Pérez, Cesar L. Cuevas-Velazquez, José L. Reyes, and Alejandra A. Covarrubias

27. Screening Intrinsically Disordered Regions for Short Linear Binding Motifs

Muhammad Ali, Leandro Simonetti, and Ylva Ivarsson

Part VII: Interactions on Surfaces

28. Probing IDP Interactions with Membranes by Fluorescence Spectroscopy

Diana Acosta, Tapojyoti Das, and David Eliezer

29. Protocol for Investigating the Interactions between Intrinsically Disordered Proteins and Membranes by Neutron Reflectometry

Alessandra Luchini and Lise Arleth

30. Interactions of IDPs with Membranes Using Dark State Exchange NMR Spectroscopy

Tapojyoti Das, Diana Acosta, and David Eliezer

Part IIX: Binding Kinetics and Mechanisms 31. Determination of Binding Kinetics of Intrinsically Disordered Proteins by Surface Plasmon Resonance Julie M. Leth and Michael Ploug

32. Measuring and Analysing Binding Kinetics of Coupled Folding and Binding Reactions under Pseudo-first Order Conditions

Kristine Steen Jensen

33. Understanding Binding Induced Folding by Temperature Jump

Angelo Toto, Francesca Troilo, Francesca Malagrinò, and Stefano Gianni

34. Determining Binding Kinetics of Intrinsically Disordered Proteins by NMR spectroscopy

Ke Yang, Munehito Arai, and Peter E. Wright

Part IX: Higher Order-Phase Separation and Fibrillation

35. Determination of Protein Phase Diagrams by Centrifugation

Nicole M. Milkovic and Tanja Mittag

36. In vitro Transition Temperature Measurement of Phase Separating Proteins by Microscopy

Jack Holland, Michael D. Crabtree, and Timothy J. Nott

37. Walking along a Protein Phase Diagram to Determine Coexistence Points by Static Light Scattering

Ivan Peran, Erik W. Martin, and Tanja Mittag

38. Expression and Purification of Intrinsically Disordered Abeta Peptide and Setup of Reproducible Aggregation Kinetics Experiment

Sara Linse

39. Measuring Interactions between Tau and Aggregation Inducers with Single Molecule Förster Resonance Energy Transfer

Sanjula P. Wickramasinghe and Elizabeth Rhoades

Part X: Modification and Targeting

40. Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins using Phos-tag SDS-PAGE

Mihkel Örd and Mart Loog

41. Multiple Site-specific Phosphorylation of IDPs Monitored by NMR

Manon Julien, Chafiaa Bouguechtouli, Ania Alik, Rania Ghouil, Sophie Zinn-Justin, and François-Xavier Theillet

42. Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins using Quantitative Mass-Spectrometry

Ervin Valk, Artemi Maljavin, and Mart Loog

43. Targeting an Intrinsically Disordered Protein by Covalent Modification

Hung Nguyen, Péter Ábrányi-Balogh, László Petri, Attila Mészáros, Kris Pauwels, Guy Vandenbussche, György Miklós Keser , and Peter Tompa

Part XI: In Cell and Interactomes

44. Recording in-cell NMR-spectra in Living Mammalian Cells

Irena Matecko-Burmann and Björn M. Burmann



45. In-cell NMR of Intrinsically Disordered Proteins in Mammalian Cells

Juan A. Gerez, Natalia C. Prymaczok, and Roland Riek

46. Analyzing IDPs in Interactomes

Vladimir N. Uversky

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