1st Edition

Protein-Solvent Interactions

Edited By Roger Gregory Copyright 1995
    592 Pages
    by CRC Press

    This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.



    1. The New Paradigm for Protein Research

    Rufus Lumry



    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


    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


    2. Solvent Interactions with Proteins Revealed by X-Ray Crystallographic Studies

    Edward N. Baker


    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



    3. Protein Hydration and Glass Transition Behavior

    Roger B. Gregory


    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



    4. Dielectric Studies of Protein Hydration

    Ronald Pethig


    Dielectric Theory and Measurements

    Experimental Results

    Protein Solutions

    Solid State Studies

    Water as Plasticizer

    Proton Conduction Effects

    Concluding Remarks


    5. Protein Dynamics: Hydration, Temperature, and Solvent Viscosity Effects Revealed by Rayleigh Scattering of Mossbauer Radiation

    Vitalii I. Goldanskii and Yurii F. Krupyanskii


    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


    6. Proteins in Essentially Nonaqueous Environments
    Darrell L. Williams, Jr., Igor Rapanovich, and Alan J. Russell


    "Anhydrous" and Heterogeneous Systems

    "Anhydrous" and Homogeneous Systems

    Water/Cosolvent Mixtures



    7. Solvent Viscosity Effect on Protein Dynamics: Updating the Concepts

    Benjamin Gavish and Saul Yedgar


    Brownian Dynamics


    Generalized Approach

    Free Volume

    Barrier Crossing

    Basic Concepts


    Viscosity Effect

    Kinetic Studies

    Ultrasonic Studies

    Why a Power Law?



    8. Effect of Solvent on Protein Internal Dynamics: The Kinetics of Ligand Binding to Myoglobin

    Wolfgang Doster, Thomas Kleinert, Frank Post, and Marcus Settles


    The Flash Photolysis Experiment

    The Kinetics of CO Binding to Myoglobin

    The Surface Barrier

    The Internal Barriers



    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


    10. Thermodynamic Mechanisms for Enthalpy-Entropy Compensation

    Ernest Grunwald and Lorrie L. Comeford


    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


    11. Preferential Interactions of Water and Cosolvents with Proteins

    Serge N. Timasheff


    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


    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



    12. Thermodynamic Nonideality and Protein Solvation

    Donald J. Winzor and Peter R. Wills


    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


    13. Molecular Basis for Protein Separations

    Rex E. Lovrien, Mark J. Conroy, and Timothy I. Richardson


    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




    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