Protein and peptide folding, misfolding, and nonfolding:
Saved in:
| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Hoboken, NJ
Wiley
2012
|
| Series: | Wiley series on protein and peptide science
13 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXII, 548 S. Ill., graph. Darst. |
| ISBN: | 9780470591697 0470591692 |
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| _version_ | 1804148858072072192 |
|---|---|
| adam_text | CONTENTS
Introduction to the Wiley Series on Protein and
Peptide
Science
xiii
Preface
xv
Contributors
xix
INTRODUCTION
1
1
Why Are We Interested in the Unfolded Peptides and Proteins?
3
Vladimir
N.
Uversky and A. Keith Dunker
1.1
Introduction,
3
1.2
Why Study IDPs?,
4
1.3
Lesson
1:
Disorderedness Is Encoded in the
Amino
Acid
Sequence and Can Be Predicted,
5
1.4
Lesson
2:
Disordered Proteins Are Highly Abundant in Nature,
7
1.5
Lesson
3:
Disordered Proteins Are Globally Heterogeneous,
9
1.6
Lesson
4:
Hydrodynamic Dimensions of Natively Unfolded
Proteins Are Charge Dependent,
14
1.7
Lesson
5:
Polymer Physics Explains Hydrodynamic Behavior
of Disordered Proteins,
16
1.8
Lesson
6:
Natively Unfolded Proteins Are Pliable and Very
Sensitive to Their Environment,
18
1.9
Lesson
7:
When Bound, Natively Unfolded Proteins Can Gain
Unusual Structures,
20
vi
CONTENTS
1.10
Lesson
8:
IDPs Can Form Disordered or Fuzzy Complexes,
25
1.11
Lesson
9:
Intrinsic Disorder Is Crucial for Recognition,
Regulation, and Signaling,
25
1.12
Lesson
10:
Protein Posttranslational Modifications Occur at
Disordered Regions,
28
1.13
Lesson
11:
Disordered Regions Are Primary Targets for AS,
30
1.14
Lesson
12:
Disordered Proteins Are Tightly Regulated in the
Living Cells,
31
1.15
Lesson
13:
Natively Unfolded Proteins Are Frequently
Associated with Human Diseases,
33
1.16
Lesson
14:
Natively Unfolded Proteins Are Attractive Drug
Targets,
35
1.17
Lesson
15:
Bright Future of Fuzzy Proteins,
38
Acknowledgments,
39
References,
40
I CONFORMATIONAL ANALYSIS OF UNFOLDED STATES
55
2
Exploring the Energy Landscape of Small Peptides and
Proteins by Molecular Dynamics Simulations
57
Gerhard Stock, Abhinav Jain, Laura Riccardi, and Phuong H. Nguyen
2.1
Introduction: Free Energy Landscapes and How to Construct
Them,
57
2.2
Dihedral Angle PCA Allows Us to Separate Internal and Global
Motion,
61
2.3
Dimensionality of the Free Energy Landscape,
62
2.4
Characterization of the Free Energy Landscape: States, Barriers,
and Transitions,
65
2.5
Low-Dimensional Simulation of Biomolecular Dynamics to
Catch Slow and Rare Processes,
67
2.6
PCA by Parts: The Folding Pathways of
Viliin
Headpiece,
69
2.7
The Energy Landscape of Aggregating
Aß-Peptides, 73
2.8
Concluding Remarks,
74
Acknowledgments,
75
References,
75
3
Local Backbone Preferences and Nearest-Neighbor Effects in the
Unfolded and Native States
79
Joe
DeBartolo,
Abhishek Jha,
Karl E
Freed, and
Tobin
R.
Sosnick
3.1
Introduction,
79
3.2
Early Days: Random Coil
—
Theory and Experiment,
80
3.3
Denatured Proteins as Self-Avoiding Random Coils,
82
3.4
Modeling the Unfolded State,
82
CONTENTS
vii
3.5 NN
Effects in Protein Structure Prediction,
86
3.6
Utilizing Folding Pathways for Structure Prediction,
87
3.7
Native State Modeling,
88
3.8
Secondary-Structure Propensities: Native Backbones in
Unfolded Proteins,
92
3.9
Conclusions,
92
Acknowledgments,
93
References,
94
4
Short-Distance FRET Applied to the Polypeptide Chain
99
Maik
H.
Jacob and Werner M.
Nau
4.1
A Short Timeline of Resonance Energy Transfer
Applied to the Polypeptide Chain,
99
4.2
A Short Theory of FRET Applied to the Polypeptide Chain,
101
4.3
DBOandDbo,
105
4.4
Short-Distance FRET Applied to the Structured Polypeptide
Chain,
107
4.5
Short-Distance FRET to Monitor Chain-Structural Transitions
upon Phosphorylation,
116
4.6
Short-Distance FRET Applied to the Structureless Chain,
120
4.7
The Future of Short-Distance FRET,
125
Acknowledgments,
125
Dedication,
126
References,
126
5
Solvation and Electrostatics as Determinants of Local
Structural Order in Unfolded Peptides and Proteins
131
Franc Avbelj
5.1
Local Structural Order in Unfolded Peptides and Proteins,
131
5.2
ESM,
134
5.3
The ESM and Strand-Coil Transition Model,
137
5.4
The ESM and Backbone Conformational Preferences,
138
5.5
The Nearest-Neighbor Effect,
141
5.6
The ESM and Cooperative Local Structures
—
Fluctuating
^-Strands,
141
5.7
The ESM and /J-Sheet Preferences in Native Proteins-
Significance of Unfolded State,
144
5.8
The ESM and Secondary Chemical Shifts of
Polypeptides,
145
5.9
Role of Backbone Solvation in Determining Hydrogen
Exchange Rates of Unfolded Polypeptides,
148
5.10
Other Theoretical Models of Unfolded Polypeptides,
148
Acknowledgments,
149
References,
149
viii CONTENTS
6
Experimental and Computational Studies of Polyproline II
Propensity
159
W. Austin Elam, Travis P.
Schrank,
and Vincent J. Hilser
6.1
Introduction,
159
6.2
Experimental Measurement of
PII
Propensities,
161
6.3
Computational Studies of Denatured State Conformational
Propensities,
168
6.4
A Steric Model Reveals Common
PII
Propensity of the
Peptide
Backbone,
172
6.5
Correlation of
PII
Propensity to
Amino
Acid Properties,
175
6.6
Summary,
180
Acknowledgments,
180
References,
180
7
Mapping Conformational Dynamics in Unfolded
Polypeptide Chains Using Short Model Peptides
by NMR Spectroscopy
187
Daniel
Mathieu,
Karin Rybka,
Jürgen Graf, and Harald Schwalbe
7.1
Introduction,
187
7.2 General
Aspects
of NMR
Spectroscopy, 189
7.3 NMR Parameters
and Their Measurement,
191
7.4
Translating NMR
Parameters
to Structural
Information, 202
7.5
Conclusions,
213
Acknowledgments,
215
References,
215
8
Secondary Structure and Dynamics of a Family of
Disordered Proteins
221
Pranesh Narayanaswami and Gary W. Daughdrill
8.1
Introduction,
221
8.2
Materials and Methods,
223
8.3
Results and Discussion,
226
Acknowledgments,
235
References,
235
II DISORDERED PEPTIDES AND MOLECULAR RECOGNITION
239
9
Binding Promiscuity of Unfolded Peptides
241
Christopher J. Oldfield, Bin Xue, A. Keith Dunker,
and Vladimir
N.
Uversky
9.1
Protein-Protein Interaction Networks,
241
9.2
Role of Intrinsic Disorder in
PPI
Networks,
242
9.3
Transient Structural Elements in Protein-Based Recognition,
243
CONTENTS ix
9.4
Chameleons and Adaptors: Binding Promiscuity of Unfolded
Peptides,
256
9.5
Principles of Using the Unfolded Protein Regions for
Binding,
262
9.6
Conclusions,
266
Acknowledgments,
266
References,
266
10
Intrinsic Flexibility of Nucleic Acid Chaperone Proteins from
Pathogenic
RNA
Viruses
279
Roland Ivanyi-Nagy,
Zuzanna Makowska,
and Jean-Luc Darlix
10.1
Introduction,
279
10.2
Retroviruses and Retroviral Nucleocapsid Proteins,
280
10.3
Core Proteins in the Flaviviridae Family of Viruses,
288
10.4
Coronavirus
Nucleocapsid Protein,
290
10.5
Hantavirus Nucleocapsid Protein,
291
Acknowledgments,
293
References,
293
III AGGREGATION OF DISORDERED PEPTIDES
307
11
Self-Assembling Alanine-Rich Peptides of
Biomedical
and
Biotechnological Relevance
309
Thomas J. Measey and
Reinhard Schweitzer-Stenner
11.1
Biomolecular Self-Assembly,
309
11.2
Misfolding and Human Disease,
310
11.3
Exploitation of
Peptide
Self-Assembly for Biotechnological
Applications,
326
11.4
Concluding Remarks,
340
Acknowledgments,
340
References,
340
12
Structural Elements Regulating Interactions in the Early Stages
of Fibrillogenesis: A Human Calcitonin Model System
351
Rosa Maria
Vitale,
Giuseppina Andreotti,
Pietro Amodeo,
and Andrea
Motta
12.1
Stating the Problem,
351
12.2
Aggregation Models: The State of The Art,
354
12.3
Human Calcitonin hCT as a Model System for
Self-Assembly,
356
12.4
The
Prefibrillar
State of hCT,
358
12.5
How Many Molecules for the Critical Nucleus?,
361
12.6
Modeling
Prefibrillar
Aggregates,
366
12.7
hCT Helical
Oligomers,
366
CONTENTS
12.8
The Role of Aromatic Residues in the Early Stages of Amyloid
Formation,
372
12.9
The Folding of hCT before Aggregation,
373
12.10
Model Explains the Differences in Aggregation Properties
between hCT and sCT,
374
12.11
hCT Fibril Maturation,
375
12.12
α
-Helix
-ȧ-Sheet Conformational
Transition and hCT
Fibrillation,
377
12.13
Concluding Remarks,
378
Acknowledgments,
378
References,
379
13
Solution NMR Studies of
Aß
Monomers and
Oligomers
389
Chunyu Wang
13.1
Introduction,
389
13.2
Overexpression and Purification of
Recombinant
АД
390
13.3
Aj3 Monomers,
393
13.4 Aß
Oligomers and Monomer-Oligomer Interaction,
403
13.5
Conclusion,
406
References,
406
14
Thermodynamic and Kinetic Models for Aggregation
of Intrinsically Disordered Proteins
413
Scott L. Crick and Rohit V. Pappu
14.1
Introduction,
413
14.2
Thermodynamics of Protein Aggregation
—
the Phase Diagram
Approach,
415
14.3
Thermodynamics of IDP Aggregation (Phase Separation)
—
MPM Description,
420
14.4
Kinetics of Homogeneous Nucleation and Elongation Using
MPMs,
425
14.5
Concepts from Colloidal Science,
427
14.6
Conclusions,
433
Acknowledgments,
433
References,
434
15
Modifiers of Protein Aggregation
—
From Nonspecific to Specific
Interactions
441
Michal
Levy-Sakin,
Roni
Scherzer-Attali, and Ehud Gazit
15.1
Introduction,
441
15.2
Nonspecific Modifiers,
442
15.3
Specific Modifiers,
454
Acknowledgments,
465
References,
466
CONTENTS xi
16
Computational Studies of Folding and Assembly
of Amyloidogenic Proteins
479
J. Srinivasa Rao, Brigita Urbane, and Luis Cruz
16.1
Introduction,
479
16.2
Amyloids,
480
16.3
Computer Simulations,
485
16.4
Summary,
514
References,
515
INDEX
529
|
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| dewey-search | 572.65 |
| dewey-sort | 3572.65 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Biologie Chemie |
| format | Book |
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| indexdate | 2024-07-10T00:13:48Z |
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| isbn | 9780470591697 0470591692 |
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| series2 | Wiley series on protein and peptide science |
| spelling | Protein and peptide folding, misfolding, and nonfolding ed. by Reinhard Schweitzer-Stenner Hoboken, NJ Wiley 2012 XXII, 548 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wiley series on protein and peptide science 13 Peptide (DE-588)4045125-2 gnd rswk-swf Strukturchemie (DE-588)4183790-3 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Peptides Protein folding (DE-588)4143413-4 Aufsatzsammlung gnd-content Proteinfaltung (DE-588)4324567-5 s Peptide (DE-588)4045125-2 s DE-604 Strukturchemie (DE-588)4183790-3 s 1\p DE-604 Schweitzer-Stenner, Reinhard edt Wiley series on protein and peptide science 13 (DE-604)BV040121525 13 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024763161&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Protein and peptide folding, misfolding, and nonfolding Wiley series on protein and peptide science Peptide (DE-588)4045125-2 gnd Strukturchemie (DE-588)4183790-3 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| subject_GND | (DE-588)4045125-2 (DE-588)4183790-3 (DE-588)4324567-5 (DE-588)4143413-4 |
| title | Protein and peptide folding, misfolding, and nonfolding |
| title_auth | Protein and peptide folding, misfolding, and nonfolding |
| title_exact_search | Protein and peptide folding, misfolding, and nonfolding |
| title_full | Protein and peptide folding, misfolding, and nonfolding ed. by Reinhard Schweitzer-Stenner |
| title_fullStr | Protein and peptide folding, misfolding, and nonfolding ed. by Reinhard Schweitzer-Stenner |
| title_full_unstemmed | Protein and peptide folding, misfolding, and nonfolding ed. by Reinhard Schweitzer-Stenner |
| title_short | Protein and peptide folding, misfolding, and nonfolding |
| title_sort | protein and peptide folding misfolding and nonfolding |
| topic | Peptide (DE-588)4045125-2 gnd Strukturchemie (DE-588)4183790-3 gnd Proteinfaltung (DE-588)4324567-5 gnd |
| topic_facet | Peptide Strukturchemie Proteinfaltung Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024763161&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV040121525 |
| work_keys_str_mv | AT schweitzerstennerreinhard proteinandpeptidefoldingmisfoldingandnonfolding |