Preface
Contributors
1. The New Paradigm for Protein Research
Rufus Lumry
Introduction
Purposes
Confusing Biology with Chemistry
Supporting Evidence
Protein Structure
Information from B Factors
Observations Based on B Factors
Information from Proton-Exchange Studies
Information About Groups from Evolution and Genetics
Information from Density Data
How Substructures Determine Getstalt Structure and Properties
Genetic Stability
Kinetic Stability
Thermodynamic Stability
"Molten-Globule" Conformation States
Structural Dependence of Common Experimental Observables
Some Devices that Became Possible After the Discovery of the Knot-Matrix Construction Principle
Modular Construction of Knot-Matrix Proteins
Expansion-Contraction Processes
Free Volume and Dielectric Constant
The "Pairing Principle"
"Completing the Knot"
Protein Activity Coefficients: Gibbs-Duhem Consequences
Intermolecular Communication Through Surfaces
Some Thermodynamic Topics of Special Importance for Biology
A Weak Relationship Between Free Energy and Its Temperature and Pressure Derivatives
Enthalpy-Entropy Compensation Behavior
Conformational Dynamics and "Dynamic Matching"
The Facts
Protein-Protein Association
The Oxygen-Binding Mechanism of Hemoglobins
Enzyme Mechanisms: Updating the Rack Mechanism
The Kunitz Proteinase Inhibitors
The Immune Reaction
Dynamical Aspects of Protein Electrostatic Potentials
The Next Level of Complexity
What Is the Atomic Description of a Knot?
What Factors Are Responsible for the Stability of Knots?
Gestalt Versus Local Fields
Summary
Thermodynamics in the Biosphere
The Evolution of Devices
Function Follows Form?
Consequences for the Immediate Future of Protein Chemistry
Hypotheses Based on the Knot-Matrix Principle
References
2. Solvent Interactions with Proteins Revealed by X-Ray Crystallographic Studies
Edward N. Baker
Introduction
Solvent Content of Protein Crystals
Crystallographic Location of Solvent
The Crystallographic Location of Solvent
The Crystallographic Method
Identification and Refinement of Solvent Sites
Chemical Identity of Solvent Molecules
Patterns of Solvent Structure
The General Picture
Hydration of Protein Groups
Internal Solvent Molecules
Surface Solvent Structure
Association with Secondary Structures
Solvent in Active Sites
Significance of Bound Solvent
Conservation of Solvent Sites
Contributions to Stability
Functional Roles of Solvent Molecules
Bound Ions and Other Solvent Molecules
Conclusions
References
3. Protein Hydration and Glass Transition Behavior
Roger B. Gregory
Introduction
Preparation of Solid State Samples
Adsorption of Water Vapor by Proteins: The Sorption Isotherm
Conventional Sorption Isotherms
Site Heterogeneity and Conformational Perturbations
Sorption Hysteresis
Identification and Coverage of Sorption Sites and Some Critical Hydration Levels in the Sorption Isotherm
Infrared Spectroscopic Studies of Protein Hydration
Heat Capacity as a Function of Hydration
Enzyme Activity
Proton Percolation
Nonfreezing Water
The Effect of Hydration on Thermal Stability
Protein Surface Areas and Monolayer Coverage
Hydration-Induced Conformational Changes
Sold State 13C NMR Studies of Protein Hydration
An X-Ray Diffraction Study of a Dehydrated Protein
FTIR Studies of Dehydration-Induced Conformational Transitions
Effect of Hydration on Protein Dynamics
Spectroscopic Methods
Hydrogen Isotope Exchange
Positron Annihilation Lifetime Spectroscopy
Glass Transitions in Proteins
Glass Transition Behavior in Polymers
Free Volume in Glass Transition Theory
The 200 K Transition in Fully Hydrated Proteins
Hydration Dependence of Glass Transition Temperatures
Hysteresis Effects
Dynamically Distinct Structural Classes in Globular Proteins
Evidence from Hydrogen Isotope Exchange
The Basis of Knot Formation
The Connection Between Hydrogen Exchange Properties and Glass Transition Behavior
"Molten Globule" and Cold-Denatured States
Protein Folding
Conclusions
References
4. Dielectric Studies of Protein Hydration
Ronald Pethig
Introduction
Dielectric Theory and Measurements
Experimental Results
Protein Solutions
Solid State Studies
Water as Plasticizer
Proton Conduction Effects
Concluding Remarks
References
5. Protein Dynamics: Hydration, Temperature, and Solvent Viscosity Effects Revealed by Rayleigh Scattering of Mossbauer Radiation
Vitalii I. Goldanskii and Yurii F. Krupyanskii
Introduction
Background of RSMR Technique, Basic Expressions, and Approximations
Hydration Dependencies of Elastic RSMR Fractions and RSMR Spectra
Solvent Composition and Viscosity Dependencies of the Elastic RSMR Spectra
Temperature Dependencies of Elastic RSMR Fraction and RSMR Spectra
Angular Dependencies of Inelastic RSMR Intensities
Properties of Protein-Bound Water
Dynamical Properties of Hydrated Proteins
Principal Conclusions and Outlook
References
6. Proteins in Essentially Nonaqueous Environments
Darrell L. Williams, Jr., Igor Rapanovich, and Alan J. Russell
Introduction
"Anhydrous" and Heterogeneous Systems
"Anhydrous" and Homogeneous Systems
Water/Cosolvent Mixtures
Conclusions
References
7. Solvent Viscosity Effect on Protein Dynamics: Updating the Concepts
Benjamin Gavish and Saul Yedgar
Introduction
Brownian Dynamics
Basics
Generalized Approach
Free Volume
Barrier Crossing
Basic Concepts
Models
Viscosity Effect
Kinetic Studies
Ultrasonic Studies
Why a Power Law?
Conclusions
References
8. Effect of Solvent on Protein Internal Dynamics: The Kinetics of Ligand Binding to Myoglobin
Wolfgang Doster, Thomas Kleinert, Frank Post, and Marcus Settles
Introduction
The Flash Photolysis Experiment
The Kinetics of CO Binding to Myoglobin
The Surface Barrier
The Internal Barriers
Conclusion
References
9. Solvent Effects on Protein Stability and Protein Association
Arieh Ben-Naim
Introduction: A Historic Perspective
Protein Folding and Protein-Protein Association
Direct and Indirect Interactions
Driving Force, Force, and Stability
Inventory of Solvent-Induced Effects
The Missing Information and How to Obtain IT
The Solvation Gibbs Energy of the Large Linear Polypeptide Having No Side Chains
Solvation of the Backbone of the F Form
Loss of the Conditional Solvation Gibbs Energies of the Various Side Chains
Pairwise Correlations
Higher-Oder Correlations
Concluding Remarks
References
10. Thermodynamic Mechanisms for Enthalpy-Entropy Compensation
Ernest Grunwald and Lorrie L. Comeford
Introduction
Experimental Examples
Interaction Mechanisms and Compensation Vector Diagrams
Examples of Partial Compensation
Thermodynamic Compensation
Molecular Species
Mathematical Formulation
Standard Partial Enthalpies and Entropies in Dilute Solutions
Molar-Shift Mechanism
Solvation Mechanism
Application to Nonpolar Solutes in Water
Delphic Dissection of Standard Partial Entropies
Concluding Remarks
References
11. Preferential Interactions of Water and Cosolvents with Proteins
Serge N. Timasheff
Introduction
Cosolvent Control of Protein Solution Stability and State of Dispersion
Binding of Cosolvent and Displacement of Reaction Equilibria
What is Binding?
Cosolvent Effects on Equilibria Relative to Water
Relation Between Preferential Interactions and Transfer Free Energy
Thermodynamic Definition of Binding
Binding Is Replacement of Water by Ligand at a Site
The Wyman Slope is the Change in Thermodynamic Interaction
Relation Between Transfer Free Energy and Preferential Interaction
How Transfer Free Energy Modulates Protein Reactions
Precipitation
Structure Stabilization-Destabilization
Why Precipitants Are Not Necessarily Stabilizers
Preferential Interactions and Binding at Sites
Classical Site Binding Theory
Inadequacy of the Site Binding Treatment
Preferential Binding as Exchange at Sites: Weak and Strong Binding
Preferential Binding as the Balance Between Water and Ligand Binding to a Protein: Meaning of Zero "Binding"
Meaning of Thermodynamic Indifference
Relation Between Global Preferential Interactions and Exchange at Sites
Direct Site Occupancy Measurements Cannot Define the Thermodynamic Interaction
Weak Effect as Results of Strong Interactions at Sites
Meaning of Sites in Weak Binding
Why Are Some Cosolvents Preferentially Excluded from Protein?
Conclusion: Competition, Compensation, Binding-Exclusion
Balance
References
12. Thermodynamic Nonideality and Protein Solvation
Donald J. Winzor and Peter R. Wills
Introduction
Quantitative Interpretation of Partial Specific Volumes
Traditional Approach
Choice of Concentration Scale
Direct Thermodynamic Interpretation
Equivalence of Treatments
Viral Coefficients from Density Measurements
Protein-Small Nonelectrolyte Systems
Osmolytes as Inert Solute
Excluded Volume Interpretation
Consideration of Small Solutes as Effective Spheres
Interpretation of Isopiestic Measurements
Freezing Point Depression Data
Frontal Gel Chromatography of Sucrose
Validity of the Proposition
Effective Thermodynamic Radii of Globular Proteins
Evaluation from Self-Covolume Measurements
Evaluation from Protein-Small Solute Covolume
Relationship to the Stokes Radius
Effects of Small Solutes on Protein Isomerization
pH-Induced Unfolding of Proteins
Ligand-Induced and Preexisting Isomerizations
Thermal Unfolding of Proteins
Concluding Remarks
References
13. Molecular Basis for Protein Separations
Rex E. Lovrien, Mark J. Conroy, and Timothy I. Richardson
Introduction
Protein Reactivity and Conformation Governance in Separations
The Plasma Albumin Prototype: Conformation Behavior, Reactivity Toward Ligands, Consequences in Coprecipitation, and Cocrystallization
Salt Counterion Contraction of Proteins from Acid-Expanded Conformation
Cocrystallization of Proteins with Inorganic and Organic Ionic Ligands
Water Inside, Water Outside Proteins
Protein Precipitation from Four-Carbon Cosolvent, t-Butanol
Matrix Coprecipitation by Organic Ion Ligands
Inorganic and Organic Ion-Binding Thermochemistry
References
Index
Biography
Roger Gregory
". . .a broad and much-needed survey of biophysical aspects of the interplay between proteins and their solvent. . . . . .uniformly well-written. . .of value to anyone with an active interest in the physical chemistry of proteins. "
---FEBS Letters
