Biothermodynamics: A
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier
2009
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
455 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XLIII, 466 S., [4] Bl. Ill., graph. Darst. |
| ISBN: | 9780123745965 |
Staff View
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| 245 | 1 | 0 | |a Biothermodynamics |n A |c ed. by Michael L. Johnson ... |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier |c 2009 | |
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Record in the Search Index
| _version_ | 1804139089300029440 |
|---|---|
| adam_text | Contents
Contributors
xi
Preface
xv
Volumes in Series
xvii
1.
Practical Approaches to Protein Folding and Assembly:
Spectroscopie
Strategies in Thermodynamics and Kinetics
1
Jad
Walters, Sara L. Milam, and A. Clay Clark
1.
Introduction
2
2.
Equilibrium Unfolding
3
3.
Measuring Folding Kinetics
21
References
36
2.
Using Thermodynamics to Understand Progesterone
Receptor Function: Method and Theory
41
Keith D. Connaghan-Jones and David
L
Bain
1.
Introduction
42
2.
Assessing Protein Functional and Structural Homogeneity
43
3.
Dissecting Linked Assembly Reactions
46
4.
Analysis and Dissection of Natural Promoters
54
5.
Measuring the Energetics of Coactivator Recruitment
62
6.
Correlation to Biological Function
64
7.
Conclusions and Future Directions
67
Acknowledgments
68
References
68
3.
Direct
Quantitäten
of Mg2
-RNA
Interactions by
Use of a Fluorescent Dye
71
Dan Grilley, Ana Maria
Soto,
and David E. Draper
1.
Introduction
72
2.
General Principles
73
3.
Ion-Binding Properties of HQS
78
4.
Preparation of Solutions and Reagents
81
5.
Instrumentation and Data Collection Protocols
84
vi
Contents
6.
Data
Analysis
88
7.
Controls
and Further Considerations
90
Acknowledgments
92
References
92
4.
Analysis of Repeat-Protein Folding Using
Nearest-Neighbor Statistical Mechanical Models
95
Turai
Aksel and Doug Barrick
1.
Historical Overview of Ising Models and Motivation
for the Present Review
96
2.
Linear Repeat Proteins and Their Connection to Linear Ising Models
97
3.
Formulating a Homopolymer Partition Function and
the Zipper Approximation
100
4.
Matrix Approach: Homopolymers
104
5.
Matrix Approach: Heteropolymers
109
6.
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding 111
7.
Matrix Homopolymer Analysis of Consensus TPR Folding
115
8.
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding
119
9.
Summary and Future Directions
123
Acknowledgments
124
References
124
5.
Isothermal
Titration
Calori
metry:
General Formalism
Using Binding Polynomials
127
Ernesto
Freire,
Arne Schön,
and Adrian Velazquez-Campoy
1.
Introduction
128
2.
The Binding Polynomial
129
3.
Microscopic Constants and Cooperativity
131
4.
Independent or Cooperative Binding?
132
5.
Analysis of
ITC Data
Using Binding Polynomials
133
6.
A Typical Case: Macromolecule with Two Ligand-Binding Sites
135
7.
Data Analysis
137
8.
Data Interpretation
141
9.
An Experimental
Exampie
146
10.
Experimental Situations from the Literature
147
11.
Macromolecule with Three Ligand-Binding Sites
150
12.
Conclusions
150
Appendix
151
Acknowledgment
154
References
154
Contents
vii
6.
Kinetic and Equilibrium Analysis of the Myosin ATPase
157
Enrique
M. De
La Cruz and E. Michael Ostap
1.
Introduction
158
2.
Reagents and Equipment Used for all Assays
159
3.
Steady-State ATPase Activity of Myosin
161
4.
Steady-State Measurement of Actomyosin Binding Affinities
166
5.
Transient Kinetic Analysis of the Individual ATPase Cycle Transitions
170
6.
Kinetic Simulations
188
Acknowledgments
189
References
190
7.
The Hill Coefficient: Inadequate Resolution of
Cooperativity in Human Hemoglobin
193
Jo M. Holt and Gary K. Ackers
1.
Introduction
194
2.
Cooperativity and Intrinsic Binding
194
3.
The Macroscopic Binding Isotherm
197
4.
The Hill Coefficient
200
5.
Microscopic Cooperativity in Hemoglobin
205
6.
Summary
211
References
212
8.
Methods for Measuring the Thermodynamic Stability
of Membrane Proteins
213
Heedeok Hong, Nathan H.
Joh,
James U. Bowie, and
Lukas
К.
Tamm
1.
Introduction
214
2.
Two Classes of Membrane Proteins
215
3.
Methods for Measuring
Transmembrane
Domain Oligomer Stability
216
4.
Methods for Measuring Multipass x-helical Membrane Protein Stability
219
5.
Methods to Study the Stability of ^-barrel Membrane Proteins
222
6.
A Few Salient Results on Forces that Stabilize Membrane Proteins
227
7.
Conclusion and Outlook
231
Acknowledgments
232
References
232
9.
NMR Analysis of Dynein Light Chain Dimerization
and Interactions With Diverse Lfgands
237
Gregory Benison and
Elisar Barbar
1.
NMR Methodology
238
2,
Monomer-dimer Equilibrium Coupled to Electrostatics
241
viii
Contents
3.
Dimerization
is Coupled to
Ugand
Binding
246
4.
Folding is Coupled to Binding
247
5.
AUostery in LC8
251
6.
Summary
255
References
256
10.
Characterization of Parvalbumin and Polcalcin
Divalent Ion Binding by Isothermal
Titration Calorimetry 259
Michael T. Henzl
1.
Introduction
260
2.
Practical Aspects of Data Collection
262
3.
Illustrative
Global
ITC
Analyses of Divalent Ion Binding
281
4.
Conclusion
295
Acknowledgment
295
References
295
11.
Energetic Profiling of Protein Folds
299
Jason Vertrees, James
0.
Wrabl, and Vincent J. Hilser
1.
Introduction
300
2.
Modeling the Native State Ensemble of Proteins using
Statistical Thermodynamics
301
3.
Energetic Profiles of Proteins Derived from Thermodynamics
of the Native State Ensemble
304
4.
Principal Components Analysis of Energetic Profile Space
306
5.
Energetic Profiles are Conserved Between Homologous Proteins
308
6.
Direct Alignment of Energetic Profiles Based on a
Variant of the
CE
Algorithm
315
7.
CE
Algorithm Described for Structure Coordinates
316
8.
Necessary Deviations from the
CE
Algorithm to Accommodate
Energetic Profiles
317
9.
Towards a Thermodynamic Homology of Fold Space:
Clustering Energetic Profiles using STEPH
318
10.
Energetic Profiles Provide a Vehicle to Discover
Conserved Substructures in the Absence of Known Homology
321
11.
Conclusion
323
Acknowledgments
325
References
325
Contents
¡χ
12.
Model Membrane Thermodynamics and Lateral Distribution of
Cholesterol: From Experimental Data To Monte Carlo Simulation
329
Juyang Huang
1.
Introduction
330
2.
Materials and Methods
331
3.
Result and Discussion
338
4.
Concluding Remarks
362
Acknowledgments
362
References
363
13.
Thinking Inside the Box: Designing, Implementing, and
Interpreting Thermodynamic Cycles to Dissect
Cooperativity in
RNA
and
DNA
Folding
365
Nathan A. Siegfried and Philip
С
Bevilacqua
1.
Introduction
366
2.
Folding Cooperativity Defined
367
3.
Thermodynamic Boxes: Design, Implementation, and Interpretation
369
4.
Thermodynamic Cubes: Design, Implementation, and Interpretation
374
5.
Examples of Cooperativity in
RNA
376
6.
Measuring Thermodynamic Parameters by UV Melting
379
7.
Concluding Remarks
390
Acknowledgment
391
References
391
14.
The Thermodynamics of Virus Capsid Assembly
395
Sarah Katen and Adam Zlotnick
1.
Introduction
396
2.
The Structural Basis of Capsid Stability
397
3.
Analysis of Capsid Stability
401
4.
Applications of Thermodynamic Evaluation of Virus Capsid Stability
408
5.
Concluding Remarks
414
References
414
15.
Extracting Equilibrium Constants from Kinetically Limited
Reacting Systems
419
John J.
Correia
and Walter F. Stafford
1.
Introduction
420
2.
Methods
421
3.
Simulation and Analysis of Dimerization
421
χ
Contents
4. Kinetically Mediated Dimerization 428
5.
A
Stepwise
Approach
436
6. Final
Thoughts
442
Acknowledgments
443
References
443
Author Index
447
Subject index
461
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| isbn | 9780123745965 |
| language | English |
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| series | Methods in enzymology |
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| spelling | Biothermodynamics A ed. by Michael L. Johnson ... 1. ed. Amsterdam [u.a.] Elsevier 2009 XLIII, 466 S., [4] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 455 Methods in enzymology ... Thermodynamik (DE-588)4059827-5 gnd rswk-swf Biomolekül (DE-588)4135124-1 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Biomolekül (DE-588)4135124-1 s Thermodynamik (DE-588)4059827-5 s b DE-604 Johnson, Michael L. 1947- Sonstige (DE-588)122328329 oth (DE-604)BV035479505 1 Methods in enzymology 455 (DE-604)BV000000938 455 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017536061&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Biothermodynamics Methods in enzymology Thermodynamik (DE-588)4059827-5 gnd Biomolekül (DE-588)4135124-1 gnd |
| subject_GND | (DE-588)4059827-5 (DE-588)4135124-1 (DE-588)4143413-4 |
| title | Biothermodynamics |
| title_auth | Biothermodynamics |
| title_exact_search | Biothermodynamics |
| title_full | Biothermodynamics A ed. by Michael L. Johnson ... |
| title_fullStr | Biothermodynamics A ed. by Michael L. Johnson ... |
| title_full_unstemmed | Biothermodynamics A ed. by Michael L. Johnson ... |
| title_short | Biothermodynamics |
| title_sort | biothermodynamics |
| topic | Thermodynamik (DE-588)4059827-5 gnd Biomolekül (DE-588)4135124-1 gnd |
| topic_facet | Thermodynamik Biomolekül Aufsatzsammlung |
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