Peter L. Privalov

Microcalorimetry of Macromolecules (eBook, ePUB)

The Physical Basis of Biological Structures

• Format: ePub

Produktbeschreibung

Examining the physical basis of the structure of macromolecules--proteins, nucleic acids, and their complexes--using calorimetric techniques Many scientists working in biology are unfamiliar with the basics of thermodynamics and its role in determining molecular structures. Yet measuring the heat of structural change a molecule undergoes under various conditions yields information on the energies involved and, thus, on the physical bases of the considered structures. Microcalorimetry of Macromolecules offers protein scientists unique access to this important information. Divided into thirteen chapters, the book introduces readers to the basics of thermodynamics as it applies to calorimetry, the evolution of the calorimetric technique, as well as how calorimetric techniques are used in the thermodynamic studies of macromolecules, detailing instruments for measuring the heat effects of various processes. Also provided is general information on the structure of biological macromolecules, proteins, and nucleic acids, focusing on the key thermodynamic problems relating to their structure. The book covers: * The use of supersensitive calorimetric instruments, including micro and nano-calorimeters for measuring the heat of isothermal reactions (Isothermal Titration Nano-Calorimeter), the heat capacities over a broad temperature range (Scanning Nano-Calorimeter), and pressure effects (Pressure Perturbation Nano-Calorimeter) * Two of the simplest but key structural elements: the alpha and polyproline helices and their complexes, the alpha-helical coiled-coil, and the pyroline coiled-coils * Complicated macromolecular formations, including small globular proteins, multidomain proteins and their complexes, and nucleic acids * Numerous examples of measuring the ground state of protein energetics, as well as changes seen when proteins interact The book also reveals how intertwined structure and thermodynamics are in terms of a macromolecule's organization, mechanism of formation, the stabilization of its three-dimensional structure, and ultimately, its function. The first book to describe microcalorimetric technique in detail, enough for graduate students and research scientists to successfully plumb the structural mysteries of proteins and the double helix, Microcalorimetry of Macromolecules is an essential introduction to using a microcalorimeter in biological studies.

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Produktdetails

• Verlag: John Wiley & Sons
• Seitenzahl: 404
• Erscheinungstermin: 29. Mai 2012
• Englisch
• ISBN-13: 9781118337493
• Artikelnr.: 37359285

Autorenporträt

PETER L. PRIVALOV is a Professor of Biology and Biophysics at the Johns Hopkins University since 1991. He received his PhD in physics from the University of Georgia, Tbilisi (former USSR), and his DrSc in biophysics from the Institute of Biophysics, Russian Academy of Sciences, Moscow. For many years, he headed the Laboratory of Thermodynamics at the Protein Research Institute of the Russian Academy of Sciences. He is the author of 230 scientific papers published in various international journals and periodicals.

Inhaltsangabe

1 Introduction 1 2 Methodology 5 2.1 Thermodynamic Basics of Calorimetry
5 2.1.1 Energy
5 2.1.2 Enthalpy
6 2.1.3 Temperature
6 2.1.4 Energy Units
7 2.1.5 Heat Capacity
8 2.1.6 Kirchhoff's Relation
9 2.1.7 Entropy
11 2.1.8 Gibbs Free Energy
13 2.2 Equilibrium Analysis
13 2.2.1 Two-State Transition
13 2.2.2 Derivatives of the Equilibrium Constant
15 2.3 Aqueous Solutions
16 2.3.1 Specifi city of Water as a Solvent
16 2.3.2 Acid-Base Equilibrium
18 2.3.3 Partial Quantities
20 2.4 Transfer of Solutes into the Aqueous Phase
23 2.4.1 Hydration Effects
23 2.4.2 Hydrophobic Force
25 2.4.3 Hydration of Polar and Nonpolar Groups
28 References
32 3 Calorimetry 33 3.1 Isothermal Reaction Microcalorimetry
33 3.1.1 The Heat of Mixing Reaction
33 3.1.2 Mixing of Reagents in Comparable Volumes
35 3.1.3 Isothermal Titration Microcalorimeter
36 3.1.4 ITC Experiments
38 3.1.5 Analysis of the ITC Data
41 3.2 Heat Capacity Calorimetry
43 3.2.1 Technical Problems
43 3.2.2 Differential Scanning Microcalorimeter
44 3.2.3 Determination of the Partial Heat Capacity of Solute Molecules
53 3.2.4 DSC Experiments
55 3.2.5 Determination of the Enthalpy of a Temperature-Induced Process
56 3.2.6 Determination of the van't Hoff Enthalpy
58 3.2.7 Multimolecular Two-State Transition
59 3.2.8 Analysis of the Complex Heat Capacity Profile
60 3.2.9 Correction for Components Refolding
61 3.3 Pressure Perturbation Calorimetry
63 3.3.1 Heat Effect of Changing Pressure
63 3.3.2 Pressure Perturbation Experiment
65 References
67 4 Macromolecules 69 4.1 Evolution of the Concept
69 4.2 Proteins
71 4.2.1 Chemical Structure
71 4.2.2 Physical Structure
76 4.2.3 Restrictions on the Conformation of Polypeptide Chains
81 4.2.4 Regular Conformations of Polypeptide Chain Proteins
82 4.3 Hierarchy in Protein Structure
86 4.3.1 Tertiary Structure of Proteins
86 4.3.2 Quaternary Structure of Proteins
88 4.4 Nucleic Acids
89 4.4.1 Chemical Structure
89 4.4.2 Physical Structure
91 References
94 5 The alpha-Helix and alpha-Helical Coiled-Coil 95 5.1 The alpha-Helix
95 5.1.1 Calorimetric Studies of alpha-Helix Unfolding-Refolding
95 5.1.2 Analysis of the Heat Capacity Function
99 5.2 alpha-Helical Coiled-Coils
105 5.2.1 Two-Stranded Coiled-Coils
105 5.2.2 Three-Stranded Coiled-Coils
110 5.3 alpha-Helical Coiled-Coil Proteins
113 5.3.1 Muscle Proteins
113 5.3.2 Myosin Rod
115 5.3.3 Paramyosin
116 5.3.4 Tropomyosin
117 5.3.5 Leucine Zipper
118 5.3.6 Discreteness of the Coiled-Coils
123 References
124 6 Polyproline-II Coiled-Coils 127 6.1 Collagens
127 6.1.1 Collagen Superhelix
127 6.1.2 Hydrogen Bonds in Collagen
129 6.1.3 Stability of Collagens
131 6.1.4 Role of Pyrrolidine Rings in Collagen Stabilization
133 6.2 Calorimetric Studies of Collagens
135 6.2.1 Enthalpy and Entropy of Collagen Melting
135 6.2.2 Correlation between Thermodynamic and Structural Characteristics of Collagens
138 6.2.3 Role of Water in Maintaining the Collagen Structure
140 6.3 Thermodynamics of Collagens
141 6.3.1 Cooperativity of Collagen Unfolding
141 6.3.2 Factors Responsible for Maintaining the Collagen Coiled-Coil
143 6.3.3 Flexibility of the Collagen Structure
145 6.3.4 Biological Aspect of the Collagen Stability Problem
148 References
150 7 Globular Proteins 153 7.1 Denaturation of Globular Proteins
153 7.1.1 Proteins at Extremal Conditions
153 7.1.2 The Main Problems of Protein Denaturation
154 7.2 Heat Denaturation of Proteins
155 7.2.1 DSC Studies of Protein Denaturation upon Heating
155 7.2.2 Reversibility of Heat Denaturation
155 7.2.3 Cooperativity of Denaturation
156 7.2.4 Heat Capacity of the Native and Denatured States
158 7.2.5 Functions Specifying Protein Stability
161 7.3 Cold Denaturation
167 7.3.1 Proteins at Low Temperatures
167 7.3.2 Experimental Observation of Cold Denaturation
168 7.4 pH-Induced Protein Denaturation
173 7.4.1 Isothermal pH Titration of Globular Proteins
173 7.5 Denaturant-Induced Protein Unfolding
175 7.5.1 Use of Denaturants for Estimating Protein Stability
175 7.5.2 Calorimetric Studies of Protein Unfolding by Denaturants
176 7.5.3 Urea and GuHCl Interactions with Protein
179 7.6 Unfolded State of Protein
182 7.6.1 Completeness of Protein Unfolding at Denaturation
182 7.6.2 Thermodynamic Functions Describing Protein States
186 References
190 8 Energetic Basis of Protein Structure 193 8.1 Hydration Effects
193 8.1.1 Proteins in an Aqueous Environment
193 8.1.2 Hydration of Protein Groups
194 8.1.3 Hydration of the Folded and Unfolded Protein
199 8.2 Protein in Vacuum
202 8.2.1 Heat Capacity of Globular Proteins
202 8.2.2 Enthalpy of Protein Unfolding in Vacuum
204 8.2.3 Entropy of Protein Unfolding in Vacuum
210 8.3 Back into the Water
214 8.3.1 Enthalpies of Protein Unfolding in Water
214 8.3.2 Hydrogen Bonds
216 8.3.3 Hydrophobic Effect
218 8.3.4 Balance of Forces Stabilizing and Destabilizing Protein Structure
219 References
223 9 Protein Folding 225 9.1 Macrostabilities and Microstabilities of Protein Structure
225 9.1.1 Macrostability of Proteins
225 9.1.2 Microstability of Proteins
226 9.1.3 Packing in Protein Interior
228 9.2 Protein Folding Technology
233 9.2.1 Intermediate States in Protein Folding
233 9.2.2 Molten Globule Concept
234 9.3 Formation of Protein Structure
241 9.3.1 Transient State in Protein Folding
241 9.3.2 Mechanism of Cooperation
242 9.3.3 Thermodynamic States of Proteins
243 References
245 10 Multidomain Proteins 249 10.1 Criterion of Cooperativity
249 10.1.1 Deviations from a Two-State Unfolding-Refolding
249 10.1.2 Papain
250 10.1.3 Pepsinogen
251 10.2 Proteins with Internal Homology
255 10.2.1 Evolution of Multidomain Proteins
255 10.2.2 Ovomucoid
255 10.2.3 Calcium-Binding Proteins
258 10.2.4 Plasminogen
263 10.2.5 Fibrinogen
264 10.2.6 Fibronectin
267 10.2.7 Discreteness in Protein Structure
268 References
271 11 Macromolecular Complexes 273 11.1 Entropy of Association Reactions
273 11.1.1 Thermodynamics of Molecular Association
273 11.1.2 Experimental Verifi cation of the Translational Entropy
275 11.2 Calorimetry of Association Entropy
277 11.2.1 SSI Dimer Dissociation
277 11.2.2 Dissociation of the Coiled-Coil
283 11.2.3 Entropy Cost of Association
285 11.3 Thermodynamics of Molecular Recognition
286 11.3.1 Calorimetry of Protein Complex Formation
286 11.3.2 Target Peptide Recognition by Calmodulin
287 11.3.3 Thermodynamic Analysis of Macromolecular Complexes
293 References
295 12 Protein-DNA Interaction 297 12.1 Problems
297 12.1.1 Two Approaches
297 12.1.2 Protein Binding to the DNA Grooves
299 12.2 Binding to the Major Groove of DNA
300 12.2.1 Homeodomains
300 12.2.2 Binding of the GCN4 bZIP to DNA
307 12.2.3 Heterodimeric bZIP Interactions with the Asymmetric DNA Site
313 12.2.4 IRF Transcription Factors
317 12.2.5 Binding of NF-kappaB to the PRDII Site
320 12.3 Binding to the Minor Groove of DNA
322 12.3.1 AT-Hooks
322 12.3.2 HMG Boxes
326 12.4 Comparative Analysis of Protein-DNA Complexes
331 12.4.1 Sequence-Specifi c versus Non-Sequence-Specifi c HMGs
331 12.4.2 Salt-Dependent versus Salt-Independent Components of Binding
336 12.4.3 Minor versus Major Groove Binding
339 12.5 Concluding Remarks
345 12.5.1 Assembling Multicomponent Protein-DNA Complex
345 12.5.2 CC Approach versus PB Theory
346 References
347 13 Nucleic Acids 353 13.1 DNA
353 13.1.1 Problems
353 13.1.2 Factors Affecting DNA Melting
354 13.2 Polynucleotides
357 13.2.1 Melting of Polynucleotides
357 13.2.2 Calorimetry of Poly(A)·Poly(U)
358 13.3 Short DNA Duplexes
361 13.3.1 Calorimetry of Short DNA Duplexes
361 13.3.2 Specifi city of the AT-rich DNA Duplexes
366 13.3.3 DNA Hydration Studied by Pressure Perturbation Calorimetry
372 13.3.4 The Cost of DNA Bending
375 13.4 RNA
376 13.4.1 Calorimetry of RNA
376 13.4.2 Calorimetric Studies of Transfer RNAs
378 References
383 Index 387