Intrinsically Disordered Protein Analysis: Volume 1, Methods and Experimental Tools

ISBN-13: 9781493962303 / Angielski / Miękka / 2016 / 511 str.

Vladimir N. Uversky; A. Keith Dunker

Opis

The last ten years' explosive development in our knowledge of IDPs is reflected in this book of the latest reproducible protocols in 'unfolded protein' research. This first volume covers a range of issues including NMR techniques and vibrational spectroscopy.

Spis treści

Part I. Assessing IDPs in the Living Cell

1. Determination of IUP Based on Susceptibility for Degradation by Default

Peter Tsvetkov and Yosef Shaul

2. In-cell NMR of Intrinsically Disordered Proteins. Prokaryotic Cells

Yutaka Ito, Tsutomu Mikawa and Brian O. Smith

3. In-cell NMR in Xenopus laevis Oocytes

Rossukon Thongwichian and Philipp Selenko

4. In-cell NMR in Mammalian Cells: Part 1

Beata Bekei, Honor May Rose, Michaela Herzig, Alexander Dose, Dirk Schwarzer, and Philipp Selenko

5. In-cell NMR in Mammalian Cells: Part 2

Beata Bekei, Honor May Rose, Michaela Herzig and Philipp Selenko

6. In-cell NMR in Mammalian Cells: Part 3

Beata Bekei, Honor May Rose, Michaela Herzig, Heike Stephanowitz, Eberhard Krause, and Philipp Selenko

7. Fourier Transform Infrared Microspectroscopy of Complex Biological Systems: from Intact Cells to Whole Organisms

Diletta Ami, Antonino Natalello, and Silvia Maria Doglia

8. Studying IDP Stability and Dynamics by Fast Relaxation Imaging in Living Cells

Apratim Dhar, Maxim Prigozhin, Hannah Gelman, and Martin Gruebele

Part II. NMR-Based Techniques

9. Measurement and Analysis of NMR Residual Dipolar Couplings for the Study of Intrinsically Disordered Proteins

Loic Salmon, Malene Ringkjøbing Jensen, Pau Bernado, Martin Blackledge

^{10. Distance Information for Disordered Proteins from NMR and ESR Measurements using Paramagnetic Spin Labels}

^{David Eliezer}

^{11. Using Chemical Shifts to Assess Transient Secondary Structure and Generate Ensemble Structures of Intrinsically Disordered Proteins}

^{Stepan Kashtanov, Wade Borcherds, Hongwei Wu, Gary W. Daughdrill, F. Marty Ytreberg}

 ^{12. Magic Angle Spinning Solid State NMR Experiments}

^{for Structural Characterization of Proteins}

 ^{Lichi Shi and Vladimir Ladizhansky}

13. Wide-line NMR and Protein Hydration

Tompa K. Bokor M. Tompa P.

14. 5-Fluorotryptophan as a Dual NMR and Fluorescent Probe of a-Synuclein

Candace M. Pfefferkorn and Jennifer C. Lee

 15. Aplpha Proton Detection Based on Backbone Assignment of Intrinsically Disordered Proteins

Part III. Vibrational Spectroscopy

16. Fourier Transform Infrared Spectroscopy of Intrinsically Disordered Proteins: Measurement Procedures and Data Analyses

Antonino Natalello, Diletta Ami, and Silvia Maria Doglia

17. Monitoring Stuctural Transitions in IDPs by Vibrational Spectroscopy of Cyanlated Cysteine

Hailiu Yang, Johnny Habchi, Sonia Longhi, Casey H. Londergan

18. Structure Analysis of Unfolded Peptides by Vibrational Circular Dichroism Spectroscopy

Reinhard Schweitzer-Stenner, Jonathan B. Soffer and Daniel Verbaro

19. Structural Analysis of Unfolded Peptides by Raman Spectroscopy

Reinhard Schweitzer-Stenner, Jonathan B. Soffer, Siobhan Toal and Daniel Verbaro

 20. Isotope-Edited Infrared Spectroscopy

Ginka S. Buchner and Jan Kubelka

Part IV. Other Spectroscopic Techniques

21. Monitoring Structural Transitions in IDPs by site-directed Spinlabeling EPR Spectroscopy

Johnny Habchi, Marlène Martinho, Antoine Gruet, Bruno Guigliarelli, Sonia Longhi and Valérie Belle

22. Circular Dichroism Techniques for the Analysis of Intrinsically

Disordered Proteins and Domains

Lucía B. Chemes, Leonardo G. Alonso, María G. Noval and Gonzalo de Prat-Gay

23. Deconstructing Time-resolved Optical Rotatory Dispersion Kinetic Measurements of Cytochrome c Folding: From Molten Globule to the Native State

Eefei Chen and David S. Kliger

 24. The use of UV-VIS Absorption Spectroscopy for Analysis of Natively Disordered Proteins

Eugene A. Permyakov

25. Intrinsic Fluorescence of Intrinsically Disordered Proteins

Paolo Neyroz and Stefano Ciurli

 26. Binding Stoichiometry and Affinity of Fluorescent Dyes to Proteins in Different Structural States

Anna I. Sulatskaya,  Olga I. Povarova,   Irina M. Kuznetsova,  Vladimir Uversky and  Konstantin K. Turoverov

27. Fluoresnece Lifetime Measurements of Intrinsically Unstructured Proteins-Applications to Alpha-Synuclein

Sarah Schreurs, Malgorzata Kluba, Jessika Meuvis, and Yves Engelborghs

28. Ensemble FRET Methods in Studies of Intrinsically Disordered Proteins

Elisha Haas

29. Fluorensce Correlation Spectroscopy to Determine the Diffusion Coefficient of the and Follow Early Formation

Sangeeta Nath, Manli Deng, and Yves Engelborghs

Blurb

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 1 includes sections on assessing IDPs in the living cell,NMR based techniques, vibrational spectroscopy, and other spectroscopic techniques. 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.