Advances in Protein Chemistry [Vol 62 - Unfolded Proteins] - G. Rose (AP, 2002) WW

421 Pages·2002·8.91 MB·English

ADVANCES IN
PROTEIN CHEMISTRY

EDITED BY

FREDERIC M. RICHARDS
DAVID S. EISENBERG

Department of Molecular Biophysics
Department of Chemistry and Biochemistry
and Biochemistry
University of California, Los Angeles
Yale University
Los Angeles, California
New Haven, Connecticut

JOHN KURIYAN

Department of Molecular Biophysics
Howard Hughes Medical Institute
Rockefeller University
1230 York Avenue
New York, NY 10021

VOLUME 62

Unfolded Proteins

EDITED BY

GEORGE D. ROSE
Department of Biophysics
Johns Hopkins University
Baltimore, Maryland

Amsterdam
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1

CONTENTS

JOHN T. EDSALL AND ADVANCES IN PROTEIN CHEMISTRY
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xi

GETTING TO KNOW U.
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xv

JOHN T. EDSALL
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xxiii

The Expanded Denatured State: An Ensemble of Conformations
Trapped in a Locally Encoded Topological Space

DAVID SHORTLE

I.
Introduction
.
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1
II.
Nuclease �131�: Local Structure
.
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4
III.
Nuclease �131�: Long-Range Structure
.
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9
IV.
Physical-Chemical Explanations of Long-Range
Structure
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14
V.
Conclusions .
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19
References
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22

Identification and Functions of Usefully Disordered Proteins

A. KEITH DUNKER, CELESTE J. BROWN, AND ZORAN OBRADOVIC

I.
Testing Whether Intrinsic Disorder Is Encoded by the
Amino Acid Sequence .
.
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26
II.
Prediction of Order and Disorder from the Amino
Acid Sequence
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37
III.
PONDR Estimations of the Commonness of Intrinsically
Disordered Proteins
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42

v

vi
CONTENTS

IV.
Functions of Intrinsically Disordered Regions
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45
V.
Conclusions .
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46
References
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46

Unfolded Proteins Studied by Raman Optical Activity

L. D. BARRON, E. W. BLANCH, AND L. HECHT

I.
Introduction
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51
II.
Raman Optical Activity Theory and Experiment.
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54
III.
Survey of Polypeptide and Protein Raman
Optical Activity
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59
IV.
Unfolded Proteins
.
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68
V.
Principal Component Analysis
.
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84
VI.
Concluding Remarks
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86
References
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86

What Fluorescence Correlation Spectroscopy Can Tell Us
about Unfolded Proteins

CARL FRIEDEN, KRISHNANANDA CHATTOPADHYAY, AND ELLIOT L. ELSON

I.
Introduction
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91
II.
Fluorescence Correlation Spectroscopy Technique
and Theory .
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93
III.
Application to Conformational Changes within the
Unfolded State
.
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100
IV.
Advantages and Disadvantages of Using Fluorescence
Correlation Spectroscopy to Study Protein
Conformational Changes
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101
V.
Experimental Studies .
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103
VI.
Concluding Remarks
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108
References
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109

Unfolded Peptides and Proteins Studied with Infrared Absorption
and Vibrational Circular Dichroism Spectra

TIMOTHY A. KEIDERLING AND QI XU

I.
Introduction
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111
II.
Experimental Techniques
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118

CONTENTS
vii

III.
Theoretical Simulation of IR and VCD Spectra .
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123
IV.
Peptide Studies
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125
V.
Protein Studies
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138
VI.
Conclusion .
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154
References
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155

Is Polyproline II a Major Backbone Conformation in Unfolded Proteins?

ZHENGSHUANG SHI, ROBERT W. WOODY, AND NEVILLE R. KALLENBACH

I.
Introduction
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163
II.
Polyproline II Dominates in Short Peptides
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164
III.
Circular Dichroism of Unfolded Proteins
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198
IV.
Summary and Broader Implications
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228
References
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233

Toward a Taxonomy of the Denatured State: Small Angle Scattering
Studies of Unfolded Proteins

IAN S. MILLETT, SEBASTIAN DONIACH, AND KEVIN W. PLAXCO

I.
Introduction
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241
II.
A Taxonomy of Unfolded States .
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242
III.
A Random-Coil Denatured State?
.
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254
IV.
Reconciling the Random Coil with a Structured
Denatured State .
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257
References
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259

Determinants of the Polyproline II Helix from Modeling Studies

TREVOR P. CREAMER AND MARGARET N. CAMPBELL

I.
Introduction
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263
II.
The Left-Handed Polyproline II Conformation .
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265
III.
Physical Determinants of the Polyproline II
Conformation
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266
IV.
Surveys of Known Protein Structures .
.
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267
V.
Modeling Studies of Polyproline II Helix Determinants
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273
VI.
Summary
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280
References
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281

viii
CONTENTS

Hydration Theory for Molecular Biophysics

MICHAEL E. PAULAITIS AND LAWRENCE R. PRATT

I.
Introduction
.
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283
II.
Potential Distribution Theorem and Preliminaries
.
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286
III.
Applications of the Potential Distribution Theorem .
.
289
IV.
The Potential Distribution Theorem Revisited
.
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297
V.
Quasi-Chemical Theory of Solutions .
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299
VI.
Primitive Quasi-Chemical Approximation .
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304
VII.
Conclusions .
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307
References
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308

Insights into the Structure and Dynamics of Unfolded Proteins
from Nuclear Magnetic Resonance

H. JANE DYSON AND PETER E. WRIGHT

I.
Introduction
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311
II.
Conformational Propensities in Peptides
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312
III.
NMR Studies of Unfolded and Partly Folded Proteins
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313
IV.
Insights into Structure and Dynamics of Unfolded States .
324
V.
Conclusions .
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337
References
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337

Unfolded State of Peptides

XAVIER DAURA, ALICE GL¨ATTLI, PETER GEE, CHRISTINE PETER,

AND WILFRED F. VAN GUNSTEREN

I.
Introduction
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341
II.
Definitions
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343
III.
A Sample of Unfolded States
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344
IV.
Epilogue
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357
References
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357

A New Perspective on Unfolded Proteins

ROBERT L. BALDWIN

I.
Introduction
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361
II.
Hydrophobic Clusters in Urea-Denatured Proteins
.
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362

CONTENTS
ix

III.
Rationale for Studying Denatured Proteins in Water .
.
362
IV.
Stiffness of the Random Chain
.
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363
V.
Preferred Backbone Conformations
.
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364
References
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366

AUTHOR INDEX .
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369

SUBJECT INDEX .
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389

This�Page�Intentionally�Left�Blank

JOHN T. EDSALL AND ADVANCES IN PROTEIN CHEMISTRY

Today the advances in almost any aspect of science are proceeding at
an ever increasing rate. There is a strong tendency for each individual to
feel that his/her area is indeed the most exciting. However, these same
individuals do not read and think any faster now than their forebears
did, with the result that science on a daily basis is breaking into smaller
and smaller segments of the overall pie. Each small segment usually
develops its own vocabulary which then inhibits easy communication
between segments, even in very similar areas. This can easily be seen
in Nature Magazine which, in just a few years, has fragmented itself into
seven or so different journals for research articles (and five separate
volumes for reviews). The number seems likely to increase markedly in
future years.
Because of this behavior at the level of the primary literature, the so-
called secondary literature (i.e., reviews) has become increasingly impor-
tant. There are two limiting major types of reviews: (1) A list of what has
been published in several different related segments over some usually
short time interval with minimal attention to tying it all together. Such
reviews can be useful, but will still be uninterpretable to those at any
distance from the general field. (2) Reviews, usually triggered by some
recent publication, but based on fundamental points, drawing on work
from diverse areas, selecting literature from studies that may go far back
in time, and resulting in a synthesis that may change the direction and
attitude of an entire field. Both types of reviews serve useful functions,
but the most sought after, and the hardest to find, are the latter.
The rising importance of the whole area of reviews is seen in the out-
put from commercial publishers and many scientific societies. This has
generated a competition for the best formats for conveying the desired

xi