ISBN-13: 9781071605264 / Angielski / Miękka / 2021 / 951 str.
ISBN-13: 9781071605264 / Angielski / Miękka / 2021 / 951 str.
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 Čalyševa, 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 pKa 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 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 26. Determining the Protective Activity of IDPs under Partial Dehydration and Freeze-thaw Conditions 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 Kristine Steen Jensen 33. Understanding Binding Induced Folding by Temperature Jump 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 Aβ 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 Keserű, and Peter Tompa Part XI: In Cell and Interactomes 44. Recording in-cell NMR-spectra in Living Mammalian Cells 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
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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