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Unfolded Proteins: From Denatured to Intrinsically Disordered
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Authors: Trevor P. Creamer (Center for Structural Biology, University of Kentucky, Lexington) 
Book Description:
The word revolution has a number of definitions (The American Heritage Dictionary, 2006). The one most pertinent to this series and volume is “a sudden or momentous change in a situation”. Recent years have seen an unprecedented explosion of interest in unfolded proteins in all of their various forms. Coupled with this increase in interest we have seen momentous changes in the way unfolded proteins are viewed. Two particular paradigms have come under close scrutiny: unfolded proteins are disordered random coils devoid of persistent structure, and protein function first requires protein structure. The first of these is currently a hotly debated subject. The second paradigm we can safely claim has been overturned.
There is a second definition of revolution that is quite relevant to a significant portion of the work reviewed herein, in particular those chapters dealing with local and persistent structure in unfolded proteins. That definition is “a turning or rotational motion about an axis” (The American Heritage Dictionary, 2006). About four decades ago, Charles Tanford (1968) demonstrated that highly denatured proteins possess hydrodynamic properties consistent with Paul Flory’s random coil (Flory, 1969). Given that the Flory random coil definition included the stipulation that conformers making up the denatured state ensemble would differ in energy by just a few kT, there has been the assumption that denatured states must therefore be completely random in nature with no persistent structure or biases towards particular conformers. Notably however, Tanford did note the random coil-like hydrodynamic data he obtained did not necessarily rule out the presence of structure in denatured proteins (Tanford, 1968). Around the same time, Sam Krimm and M. Lois Tiffany noted that the CD spectra they obtained for proteins in the presence of high concentration of chemical denaturants had similarities to spectra obtained for homopolymers of proline, lysine, and glutamic acid in water (Tiffany and Krimm, 1968a, 1968b, 1973, 1974). Homopolymers of these residues were known to adopt the left-handed polyproline II conformation, leading Tiffany and Krimm to hypothesize that highly denatured proteins possess significant polyproline II helix content. Of these two views, that espousing the lack of structure in denatured proteins became more widely adopted and was, over time, adopted as a central paradigm in protein folding. As several of the chapters in this volume note, a Tiffany and Krimm-like view appears to be, to some extent, the more correct one. The level to which it is correct is still unknown, although it is clear that the polyproline II helical conformation is not the only, perhaps not even the most common, persistent conformation present in unfolded proteins. Thus we have come through a full circle or revolution. (from the preface)

Table of Contents:
Preface

Chapter 1 - The Denatured States of Proteins: How Random are They?; pp. 1-21
(David Shortle, The Johns Hopkins University School of Medicine, Maryland)

Chapter 2 - Thermodynamic Approaches to Understanding Protein Denatured States; pp. 23-50
(Bruce E. Bowler, Department of Chemistry and Center for Biomolecular Structure and Dynamics, University of Montana, USA)

Chapter 3 - Non-native electrostatic interactions in the denatured state ensemble: Effects on protein stability and folding; pp. 51-69
(Jae-Hyun Cho, Columbia University, NY, Satoshi Sato, Okayama Research Park Incubation Center, Okayama, Daniel P. Raleigh, State University of New York at Stony Brook, NY, USA)

Chapter 4 - Conformational Analysis of Unfolded States of Peptides by UV-CD and NMR; pp. 71-99
(Kang Chen†, Zhigang Liu, New York University, NY, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Clay Bracken, Weill Medical College of Cornell University, NY,)

Chapter 5 - Conformational Analysis of Unfolded Peptides by Vibrational Spectroscopy; pp. 101-141
(Reinhard Schweitzer-Stenner, Department of Chemistry, Drexel University, Philadelphia, USA)

Chapter 6 - Studies of protein disordered states using peptide model systems; pp. 143-167
(Veronique M. Chellgren, Brian W. Chellgren, Trevor P. Creamer, Center for Structural Biology, University of Kentucky, Lexington, USA)

Chapter 7 - Calorimetric Determination of the Thermodynamics of Polyproline II (PII) Helix Formation in the Unfolded States of Protein; pp. 169-193
(Steven T. Whitten, University of Texas Medical Branch, Texas, RedStorm Scientific, Inc., Texas, Josephine C. Ferreon, James B. Hamburger, University of Texas Medical Branch, Texas)

Chapter 8 - Global versus local features of an unfolded peptide system – Aâ42 modeled by Dynamics simulations and NMR experiments; pp. 195-212
(Nikolaos G. Sgourakis, Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Angel E. Garcia, Center for Biotechnology and Interdisciplinary Studies, Dept. of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, NY)

Chapter 9 - Residual structure and binding functions of intrinsically disordered proteins; pp. 213-235
(Peter Tompa, Monika Fuxreiter, Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences)

Chapter 10 - Natively Unfolded Proteins; pp. 237-294
(Vladimir N. Uversky, Indiana University School of Medicine, USA, Institute for Biological Instrumentation, Russian Academy of Sciences, Russia)

Index

   Series:
      Scientific Revolutions - Vladimir N. Uversky (University of South Florida, USA), Series Editor
   Binding: Hardcover
   Pub. Date: 2008
   ISBN: 978-1-60456-107-4
   Status: AV
  
Status Code Description
AN Announcing
FM Formatting
PP Page Proofs
FP Final Production
EP Editorial Production
PR At Prepress
AP At Press
AV Available
  
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Unfolded Proteins: From Denatured to Intrinsically Disordered