Advances in Protein Chemistry [Vol 62 - Unfolded Proteins] - G. Rose (AP, Bio Med 1
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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 Boston London New York Oxford Paris
San Diego San Francisco Singapore Sydney Tokyo
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∞
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C
2002, Elsevier Science (USA).
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CONTENTS
JOHN T
.
EDSALL AND ADVANCES IN PROTEIN CHEMISTRY
. . .
xi
. . . . . . . . . .
GETTING TO KNOW U
xv
JOHN T
.
EDSALL
. . . . . . . . . .
xxiii
The Expanded Denatured State: An Ensemble of Conformations
Trapped in a Locally Encoded Topological Space
D
AVID
S
HORTLE
I. Introduction
. . . . . . . . .
1
II. Nuclease
131
: Local Structure
. . . . .
4
III. Nuclease
131
: Long-Range Structure
. . . .
9
IV. Physical-Chemical Explanations of Long-Range
Structure
. . . . . . . . . .
14
V. Conclusions
. . . . . . . . . .
19
References
. . . . . . . . . .
22
Identification and Functions of Usefully Disordered Proteins
A. K
EITH
D
UNKER
,C
ELESTE
J. B
ROWN
,
AND
Z
ORAN
O
BRADOVIC
I. Testing Whether Intrinsic Disorder Is Encoded by the
Amino Acid Sequence
. . . . . . . .
26
II. Prediction of Order and Disorder from the Amino
Acid Sequence
. . . . . . . . .
37
III. PONDR Estimations of the Commonness of Intrinsically
Disordered Proteins
. . . . . . . .
42
v
vi
CONTENTS
IV. Functions of Intrinsically Disordered Regions
. . .
45
V. Conclusions
. . . . . . . . . .
46
References
. . . . . . . . . .
46
Unfolded Proteins Studied by Raman Optical Activity
L. D. B
ARRON
,E.W.B
LANCH
,
AND
L. H
ECHT
I. Introduction
. . . . . . . . .
51
II. Raman Optical Activity Theory and Experiment
. . .
54
III. Survey of Polypeptide and Protein Raman
Optical Activity
. . . . . . . . .
59
IV. Unfolded Proteins
. . . . . . . .
68
V. Principal Component Analysis
. . . . . .
84
VI. Concluding Remarks
. . . . . . . .
86
References
. . . . . . . . . .
86
What Fluorescence Correlation Spectroscopy Can Tell Us
about Unfolded Proteins
C
ARL
F
RIEDEN
,K
RISHNANANDA
C
HATTOPADHYAY
,
AND
E
LLIOT
L. E
LSON
I. Introduction
. . . . . . . . .
91
II. Fluorescence Correlation Spectroscopy Technique
and Theory
. . . . . . . . . .
93
III. Application to Conformational Changes within the
Unfolded State
. . . . . . . . .
100
IV. Advantages and Disadvantages of Using Fluorescence
Correlation Spectroscopy to Study Protein
Conformational Changes
. . . . . . .
101
V. Experimental Studies
. . . . . . . .
103
VI. Concluding Remarks
. . . . . . . .
108
References
. . . . . . . . . .
109
Unfolded Peptides and Proteins Studied with Infrared Absorption
and Vibrational Circular Dichroism Spectra
T
IMOTHY
A. K
EIDERLING AND
Q
I
X
U
I. Introduction
. . . . . . . . .
111
II. Experimental Techniques
. . . . . . .
118
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