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Intrinsically Disordered Protein Analysis

Intrinsically Disordered Protein Analysis

Volume 2, Methods and Experimental Tools


Methods in Molecular Biology

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Over the past decade, there has been an explosive development of research of intrinsically disordered proteins (IDPs), which are also known as unfolded proteins. Structural biologists now recognize that the functional diversity provided by disordered regions complements the functional repertoire of ordered protein regions. In Intrinsically Disordered Protein Analysis: Methods and Experimental Tools , expert researchers explore the high abundance of IDPs in various organisms, their unique structural features, numerous functions, and crucial associations with different diseases. Volume 2 includes sections on single molecule techniques, methods to assess protein size and shape, analyzing conformational behavior, mass-spectrometry, expression and purification of IDP’s. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Thorough and intuitive, Intrinsically Disordered Protein Analysis: Methods and Experimental Tools helps scientists further their investigations of these fascinating and dynamic molecules.


Part I. Single Molecule Techniques

1. Immobilization of Proteins for Single Molecule Fluorescence Resonance Energy Transfer Measurements of Conformation and Dynamics

Ucheor B. Choi, Keith R. Weninger, and Mark E. Bowen

2. Application of Confocal Single Molecule FRET to Intrinsically Disordered Proteins

Benjamin Schuler, Sonja Müller-Späth, Andrea Sorranno, Daniel Nettles

3. Single-Molecule Force Spectroscopy of Chimeric Polyprotein Constructs Containing Intrinsically Disordered Domains

Marco Brucale, Isabella Tessari, Luigi Bubacco, Bruno Samorì

4. Visualization of Mobility by Atomic Force Microscopy

Toshio Ando and Noriyuki Kodera

5. Unequivocal Single-Molecule Force Spectroscopy of Intrinsically Disordered Proteins

Javier Oroz, Rubén Hervás, Alejandro Valbuena & Mariano Carrión-Vázquez

Part II. Methods to Assess Protein Size and Shape

6. Sedimentation Velocity Analytical Ultracentrifugation for Intrinsically Disordered Proteins

Andrés G. Salvay, Guillaume Communie, and Christine Ebel

7. Analysis of Intrinsically Disordered Proteins by Small-Angle X-ray Scattering

Pau Bernadó and Dmitri I. Svergun

8. Small Angle Neutron Scattering (SANS) for the Structural Study of Intrinsically Disordered Proteins in Solution: a Practical Guide

Frank Gabel

9. Dynamic and Static Light Scattering of Intrinsically Disordered Proteins

Klaus Gast and Christian Fiedler

10. Estimation of Intrinsically Disordered Protein Shape and Time-averaged Apparent Hydration in Native Conditions by a Combination of Hydrodynamic Methods

Johanna C. Karst, Ana Cristina Sotomayor-Pérez, Daniel Ladant and Alexandre Chenal

11. Size-Exclusion Chromatography in Structural Analysis of Intrinsically Disordered Proteins

Vladimir N. Uversky

Part III. Methods to Analyze Conformational Behavior

12. Denaturant-induced Conformational Transitions in Intrinsically Disordered Proteins

Paolo Neyroz, Stefano Ciurli, and Vladimir N. Uversky

13. Identification of Intrinsically Disordered Proteins by a Special 2D Electrophoresis

Agnes Tantos, Peter Tompa

14. pH-induced Changes in Intrinsically-disordered Proteins

Matthew D. Smith and Masoud Jelokhani-Niaraki

15. Temperature Induced Transitions in Disordered Proteins Probed by NMR Spectroscopy

Magnus Kjaergaard, Flemming M. Poulsen and Birthe B. Kragelund

16. Analyzing Temperature Induced Transitions in Disordered Proteins by NMR Spectroscopy and Secondary Chemical Shift Analyses

Magnus Kjaergaard, Flemming M. Poulsen & Birthe B. Kragelund

17. Osmolyte-, Binding-, and Temperature-Induced Transitions of Intrinsically Disordered Proteins

Allan Chris M. Ferreon and Ashok A. Deniz

18. Laser Temperature-jump Spectroscopy of Intrinsically Disordered Proteins

Stephen J. Hagen

19. Differential Scanning Microcalorimetry of Intrinsically Disordered Proteins

Sergei E. Permyakov

20. Identifying Disordered Regions in Proteins by Limited Proteolysis

Angelo Fontana, Patrizia Polverino de Laureto, Barbara Spolaore and Erica Frare

21. The Effect of Counter Ions on the Conformation of Intrinsically Disordered Proteins Studied by Size-exclusion Chromatography

Magdalena Wojtas, Tomasz M. Kapłon, Piotr Dobryszycki, Andrzej Ożyhar

22. Mean Net Charge of Intrinsically Disordered Proteins: Experimental Determination of Protein Valence by Electrophoretic Mobility Measurements

Ana Cristina Sotomayor-Pérez, Johanna C. Karst, Daniel Ladant and Alexandre Chenal

23. Protein Characterization by Partitioning in Aqueous Two-Phase Systems

Larissa Mikheeva, Pedro Madeira, and Boris Zaslavsky

Part IV. Mass-Spectrometry

24. Detection and Characterization of Large-scale Protein Conformational Transitions in Solution using Charge-state Distribution Analysis in ESI-MS

Rinat R. Abzalimov, Agya K. Frimpong and Igor A. Kaltashov

25. Localizing Flexible Regions in Proteins using Hydrogen Deuterium Exchange Mass Spectrometry

Cedric E. Bobst and Igor A. Kaltashov

26. Mass-spectrometry Tools for Analysis of Intermolecular Interactions

Jared R. Auclair, Mohan Somasundaran, Karin M. Green, James E. Evans, Celia A. Schiffer, Dagmar Ringe, Gregory A. Petsko, and Jeffrey N. Agar

27. Characterization of Oligomerization- Aggregation Products of Neurodegenerative Target Proteins by Ion Mobility Mass Spectrometry

Camelia Vlad, Marius Ionut Iurascu, Stefan Slamnoiu, Bastian Hengerer, and Michael Przybylski

Part V. Expression and Purification of IDP's

28. Identifying Solubility-promoting Buffers for Intrinsically Disordered Proteins Prior to Purification

Kelly A. Churion and Sarah E. Bondos

29. Proteomic Methods for the Identification of Intrinsically Disordered Proteins

Agnes Tantos, Peter Tompa

30. Selective Isotope Labeling of Recombinant Proteins in E. coli

Kit I. Tong, Masayuki Yamamoto, and Toshiyuki Tanaka

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