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Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation

ISBN: 978-0-470-34341-8
760 pages
April 2010
Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation (0470343419) cover image
Instrumental techniques for analyzing intrinsically disordered proteins

The recently recognized phenomenon of protein intrinsic disorder is gaining significant interest among researchers, especially as the number of proteins and protein domains that have been shown to be intrinsically disordered rapidly grows. The first reference to tackle this little-documented area, Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation provides researchers with a much-needed, comprehensive summary of recent achievements in the methods for structural characterization of intrinsically disordered proteins (IDPs).

Chapters discuss:

  • Assessment of IDPs in the living cell

  • Spectroscopic techniques for the analysis of IDPs, including NMR and EPR spectroscopies, FTIR, circular dichroism, fluorescence spectroscopy, vibrational methods, and single-molecule analysis

  • Single-molecule techniques applied to the study of IDPs

  • Assessment of IDP size and shape

  • Tools for the analysis of IDP conformational stability

  • Mass spectrometry

  • Approaches for expression and purification of IDPs

With contributions from an international selection of leading researchers, Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation fills an important need in a rapidly growing field. It is required reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, physiologists, and specialists in drug design and development, proteomics, and molecular medicine with an interest in proteins and peptides.

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PREFACE.

INTRODUCTION TO THE WILEY SERIES ON PROTEIN AND PEPTIDE SCIENCE.

LIST OF CONTRIBUTORS.

LIST OF ABBREVIATIONS.

PART I ASSESSING IDPs IN THE LIVING CELL.

1 IDPs and Protein Degradation in The Cell (Yosef Shaul, Peter Tsvetkov, and Nina Reuven).

2 The Structural Biology of IDPs Inside Cells (Philipp Selenko).

PART II SPECTROSCOPIC TECHNIQUES.

3 Nuclear Magnetic Resonance Spectroscopy Applied to (Intrinsically) Disordered Proteins (Frans A. A. Mulder, Martin Lundqvist, and Ruud M. Scheek).

4 Atomic-Level Characterization of Disordered Protein Ensembles Using NMR Residual Dipolar Couplings (Martin Blackledge, Pau Bernadó, and Malene Ringkjøbing Jensen).

5 Determining Structural Ensembles for Intrinsically Disordered Proteins (Gary W. Daughdrill).

6 Site-Directed Spin Labeling EPR Spectroscopy (Valérie Belle,, Sabrina Rouger, Stéphanie Costanzo, Sonia Longhi, and André Fournel).

7 The Structure of Unfolded Peptides and Proteins Explored by Vibrational Spectroscopy (Reinhard Schweitzer-Stenner, Thomas J. Measey, Andrew M. Hagarman, and Isabelle C. Dragomir).

8 Intrinsically Disordered Proteins and Induced Folding Studied by Fourier Transform Infrared Spectroscopy (Antonino Natalello and Silvia Maria Doglia).

9 Genetically Engineered Polypeptides as a Model of Intrinsically Disordered Fibrillogenic Proteins: Deep UV Resonance Raman Spectroscopic Study (Natalya I. Topilina, Vitali Sikirzhytski, Seiichiro Higashiya, Vladimir V. Ermolenkov, John T. Welch, and Igor K. Lednev).

10 Circular Dichroism of Intrinsically Disordered Proteins (Robert W. Woody).

11 Fluorescence Spectroscopy of Intrinsically Disordered Proteins (Eugene A. Permyakov and Vladimir N. Uversky).

12 Hydration of Intrinsically Disordered Proteins From Wide-Line NMR (Kálmán Tompa, Monika Bokor, and Peter Tompa).

PART III SINGLE-MOLECULE TECHNIQUES.

13 Single-Molecule Spectroscopy of Unfolded Proteins (Benjamin Schuler).

14 Monitoring the Conformational Equilibria of Monomeric Intrinsically Disordered Proteins by Single-Molecule Force Spectroscopy (Massimo Sandal, Marco Brucale, and Bruno Samorì).

PART IV METHODS TO ASSESS PROTEIN SIZE AND SHAPE.

15 Analytical Ultracentrifugation, a Useful Tool to Probe Intrinsically Disordered Proteins (Florence Manon and Christine Ebel).

16 Structural Insights into Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering (Pau Bernadó and Dmitri I. Svergun).

17 Dynamic and Static Light Scattering (Klaus Gast).

18 Analyzing Intrinsically Disordered Proteins by Size Exclusion Chromatography (Vladimir N. Uversky).

PART V CONFORMATIONAL STABILITY 545

19 Conformational Behavior of Intrinsically Disordered Proteins: Effects of Strong Denaturants, Temperature, PH, Counterions, and Macromolecular Crowding (Vladimir N. Uversky).

20 Detecting Disordered Regions in Proteins by Limited Proteolysis (Angelo Fontana, Patrizia Polverino de Laureto, Barbara Spolaore, Erica Frare, and Marcello Zambonin).

PART VI MASS SPECTROMETRY.

21 Mass Spectrometry Tools for the Investigation of Structural Disorder and Conformational Transitions in Proteins (Mária Šamalíková, Carlo Santambrogio, and Rita Grandori).

PART VII EXPRESSION AND PURIFICATION OF IDPS.

22 Recombinant Production of Intrinsically Disordered Proteins for Biophysical and Structural Characterization (Dmitri Tolkatchev, Josee Plamondon, Richard Gingras, Zhengding Su, and Feng Ni).

23 Large-Scale Identifi cation of Intrinsically Disordered Proteins (Vladimir N. Uversky, Marc S. Cortese, Peter Tompa, Veronika Csizmok, and A. Keith Dunker).

24 Purification of Intrinsically Disordered Proteins (Aviv Paz, Tzviya Zeev-Ben-Mordehai, Joel L. Sussman, and Israel Silman).

INDEX.

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Vladimir N. Uversky, PhD, is a Senior Research Professor at the Indiana University School of Medicine. He obtained his academic degrees from Moscow Institute of Physics and Technology (PhD) and the Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences. Professor Uversky has authored over 300 scientific publications and edited several books and book series on protein structure, function, folding, and misfolding. He is also an editor of several scientific journals.

Sonia Longhi, PhD, is a Director of Research at the Center for the National Scientific Research (CNRS), heading the Structural Disorder and Molecular Recognition group within the AFMB laboratory. She obtained her PhD from the Università degli Studi of Milan in 1993. She has authored more than sixty scientific publications and edited a book on measles virus nucleoprotein.

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"With contributions from an international selection of leading researchers, this book fills an important need in a rapidly growing field. It is required reading for biochemists, biophysicists, molecular biologists, geneticists, cell biologists, physiologists, and specialists in drug design and development, proteomics, and molecular medicine with an interest in proteins and peptides." (Anticancer Research, 1 August 2010)
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