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Biothermodynamics Part A, Volume 455 [Kietas viršelis]

Edited by (Washington University School of Medicine, St. Louis, Mo, USA), Edited by (Washington University Medical Center, St. Louis, MO, USA), Edited by (University of Virginia Health Sciences Center, Charlottesville, USA)
  • Formatas: Hardback, 996 pages, aukštis x plotis: 229x152 mm, weight: 950 g
  • Serija: Methods in Enzymology
  • Išleidimo metai: 23-Apr-2009
  • Leidėjas: Academic Press Inc
  • ISBN-10: 0123745969
  • ISBN-13: 9780123745965
Kitos knygos pagal šią temą:
Biothermodynamics Part A, Volume 455Didesnis paveikslėlis
  • Formatas: Hardback, 996 pages, aukštis x plotis: 229x152 mm, weight: 950 g
  • Serija: Methods in Enzymology
  • Išleidimo metai: 23-Apr-2009
  • Leidėjas: Academic Press Inc
  • ISBN-10: 0123745969
  • ISBN-13: 9780123745965
Kitos knygos pagal šią temą:
Pastovi nuoroda: https://www.kriso.lt/db/9780123745965.html
Raktažodžiai:
In the last several years there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions.

In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions.

The use of thermodynamics in biological research is used as an “energy book-keeping system.? While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the
pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well.

Daugiau informacijos

This volume presents robust and modern thermodynamic methods for determining the "functional energetics" of macromolecular structures with their biological functions.
Contributors xi
Preface xv
Volumes in Series xvii
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics
1(40)
Jad Walters
Sara L. Milam
A. Clay Clark
Introduction
2(1)
Equilibrium Unfolding
3(18)
Measuring Folding Kinetics
21(20)
References
36(5)
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory
41(30)
Keith D. Connaghan-Jones
David L. Bain
Introduction
42(1)
Assessing Protein Functional and Structural Homogeneity
43(3)
Dissecting Linked Assembly Reactions
46(8)
Analysis and Dissection of Natural Promoters
54(8)
Measuring the Energetics of Coactivator Recruitment
62(2)
Correlation to Biological Function
64(3)
Conclusions and Future Directions
67(4)
Acknowledgments
68(1)
References
68(3)
Direct Quantitation of Mg2+-RNA Interactions by Use of a Fluorescent Dye
71(24)
Dan Grilley
Ana Maria Soto
David E. Draper
Introduction
72(1)
General Principles
73(5)
Ion-Binding Properties of HQS
78(3)
Preparation of Solutions and Reagents
81(3)
Instrumentation and Data Collection Protocols
84(4)
Data Analysis
88(2)
Controls and Further Considerations
90(5)
Acknowledgments
92(1)
References
92(3)
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models
95(32)
Tural Aksel
Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
96(1)
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(2)
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
111(4)
Matrix Homopolymer Analysis of Consensus TPR Folding
115(4)
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding
119(4)
Summary and Future Directions
123(4)
Acknowledgments
124(1)
References
124(3)
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials
127(30)
Ernesto Freire
Arne Schon
Adrian Velazquez-Campoy
Introduction
128(1)
The Binding Polynomial
129(2)
Microscopic Constants and Cooperativity
131(1)
Independent or Cooperative Binding?
132(1)
Analysis of ITC Data Using Binding Polynomials
133(2)
A Typical Case: Macromolecule with Two Ligand-Binding Sites
135(2)
Data Analysis
137(4)
Data Interpretation
141(5)
An Experimental Example
146(1)
Experimental Situations from the Literature
147(3)
Macromolecule with Three Ligand-Binding Sites
150(1)
Conclusions
150(7)
Appendix
151(3)
Acknowledgment
154(1)
References
154(3)
Kinetic and Equilibrium Analysis of the Myosin ATPase
157(36)
Enrique M. De La Cruz
E. Michael Ostap
Introduction
158(1)
Reagents and Equipment Used for all Assays
159(2)
Steady-State ATPase Activity of Myosin
161(5)
Steady-State Measurement of Actomyosin Binding Affinities
166(4)
Transient Kinetic Analysis of the Individual ATPase Cycle Transitions
170(18)
Kinetic Simulations
188(5)
Acknowledgments
189(1)
References
190(3)
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin
193(20)
Jo M. Holt
Gary K. Ackers
Introduction
194(1)
Cooperativity and Intrinsic Binding
194(3)
The Macroscopic Binding Isotherm
197(3)
The Hill Coefficient
200(5)
Microscopic Cooperativity in Hemoglobin
205(6)
Summary
211(2)
References
212(1)
Methods for Measuring the Thermodynamic Stability of Membrane Proteins
213(24)
Heedeok Hong
Nathan H. Joh
James U. Bowie
Lukas K. Tamm
Introduction
214(1)
Two Classes of Membrane Proteins
215(1)
Methods for Measuring Transmembrane Domain Oligomer Stability
216(3)
Methods for Measuring Multipass α-helical Membrane Protein Stability
219(3)
Methods to Study the Stability of β-barrel Membrane Proteins
222(5)
A Few Salient Results on Forces that Stabilize Membrane Proteins
227(4)
Conclusion and Outlook
231(6)
Acknowledgments
232(1)
References
232(5)
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands
237(22)
Gregory Benison
Elisar Barbar
NMR Methodology
238(3)
Monomer-dimer Equilibrium Coupled to Electrostatics
241(5)
Dimerization is Coupled to Ligand Binding
246(1)
Folding is Coupled to Binding
247(4)
Allostery in LC8
251(4)
Summary
255(4)
References
256(3)
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry
259(40)
Michael T. Henzl
Introduction
260(2)
Practical Aspects of Data Collection
262(19)
Illustrative Global ITC Analyses of Divalent Ion Binding
281(14)
Conclusion
295(4)
Acknowledgment
295(1)
References
295(4)
Energetic Profiling of Protein Folds
299(30)
Jason Vertrees
James O. Wrabl
Vincent J. Hilser
Introduction
300(1)
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(2)
Principal Components Analysis of Energetic Profile Space
306(2)
Energetic Profiles are Conserved Between Homologous Proteins
308(7)
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
315(1)
CE Algorithm Described for Structure Coordinates
316(1)
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
317(1)
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using Steph
318(3)
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
321(2)
Conclusion
323(6)
Acknowledgments
325(1)
References
325(4)
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation
329(36)
Juyang Huang
Introduction
330(1)
Materials and Methods
331(7)
Result and Discussion
338(24)
Concluding Remarks
362(3)
Acknowledgments
362(1)
References
363(2)
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding
365(30)
Nathan A. Siegfried
Philip C. Bevilacqua
Introduction
366(1)
Folding Cooperativity Defined
367(2)
Thermodynamic Boxes: Design, Implementation, and Interpretation
369(5)
Thermodynamic Cubes: Design, Implementation, and Interpretation
374(2)
Examples of Cooperativity in RNA
376(3)
Measuring Thermodynamic Parameters by UV Melting
379(11)
Concluding Remarks
390(5)
Acknowledgment
391(1)
References
391(4)
The Thermodynamics of Virus Capsid Assembly
395(24)
Sarah Katen
Adam Zlotnick
Introduction
396(1)
The Structural Basis of Capsid Stability
397(4)
Analysis of Capsid Stability
401(7)
Applications of Thermodynamic Evaluation of Virus Capsid Stability
408(6)
Concluding Remarks
414(5)
References
414(5)
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems
419(28)
John J. Correia
Walter F. Stafford
Introduction
420(1)
Methods
421(1)
Simulation and Analysis of Dimerization
421(7)
Kinetically Mediated Dimerization
428(8)
A Stepwise Approach
436(6)
Final Thoughts
442(5)
Acknowledgments
443(1)
References
443(4)
Author Index 447(14)
Subject Index 461