Protein Structure

1st Edition, Volume 1 - January 1, 1961

Author: Harold A. Scheraga

Editors: Nathan O. Kaplan, Harold A. Scheraga

eBook ISBN:

9 7 8 - 1 - 4 8 3 2 - 5 8 9 7 - 3

Protein Structure deals with the chemistry and physics of biologically important molecules—the proteins—particularly the determination of the structure of various proteins, their… Read more

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Protein Structure deals with the chemistry and physics of biologically important molecules—the proteins—particularly the determination of the structure of various proteins, their thermodynamics, their kinetics, and the mechanisms of different reactions of individual proteins. The book approaches the study of protein structure in two ways: firstly, by determining the general features of protein structure, the overall size, and shape of the molecule; and secondly, by investigating the molecule internally along with the various aspects of the internal configuration of protein molecules. It describes in detail experimental methods for determining protein structure in solution, such as the hydrodynamic method, the thermodynamic optical method, and the electrochemical method. The book then explains the results of experiments carried out on insulin, lysozyme, and ribonuclease. The text notes that the experiments, carried out on native and denatured proteins as well as on derivatives prepared by chemical modification (e.g., by methylation, iodination, acetylation, etc.), can lead to greater understanding of secondary and tertiary structures of proteins of known sequence. The book is suitable for biochemists, micro-biologists, cellular researchers, or investigators involved in protein structure and other biological sciences related to muscle physiologists, geneticists, enzymologists, or immunologists.

PrefaceIntroductionI. Hydrodynamic Properties of Protein Solutions 1. Hydrodynamic Quantities 2. Hydrodynamic Theories 3. Intrinsic Viscosity—Translational Frictional Coefficient 4. Intrinsic Viscosity—Rotational Frictional Coefficient 5. Translational Frictional Coefficient—Rotational Frictional Coefficient 6. Partial Molai Volume 7. Hydrodynamic versus Thermodynamic Quantities 8. Examples 9. Flexible Chain Molecules 10. Correction for Heterogeneity General ReferencesII. Internal Structure; Effect of Hydrogen Bonding on Side-Chain Reactivity 1. Internal Structure Problem 2. The Hydrophobie Bond 3. Side-Chain Hydrogen Bonding 4. The Protein Model 5. Hydrogen Bond Strength 6. Ionization—Heterologous Single Bonds 7. Ionization—Homologous Single Bonds 8. Ionization—Homologous Double Bonds 9. Ionization—Competition 10. Ionization—Cooperative Bonding 11. Carboxyl Ionization in Bovine Serum Albumin 12. Binding of Small Molecules and Ions 13. Additional Remarks General ReferencesIII. Limited Proteolysis 1. Model Involving Hydrogen Bonds 2. Stabilization by One Hydrogen Bond 3. Stabilization by Several Hydrogen Bonds 4. Magnitude of Peptide Bond Stabilization 5. Role of Denaturation 6. Cyclic Stabilization 7. Additional Remarks General ReferenceIV. Denaturation 1. Definition of Denaturation 2. Ordered and Disordered States 3. Elastic Properties of Protein Fibers a. Relative Lengths of a Polypeptide Chain b. Observations on Shrinkage in Fibers c. Model for Protein Fiber d. The Flory-Gee Equation e. Integration of the Flory-Gee Equation f. Magnitude and pH Dependence of △h' g. Evaluation of Tcm h. Equilibrium Force-Temperature Curves i. Effect of Salts, Urea, etc j. Effect of Swelling k. Experimental Behavior 4. Equilibrium in Solution a. Model for Reversible Denaturation b. Thermodynamic Formulation c. pH Dependence d. Over-All Free Energy Change e. Effect of Salts, Urea, etc f. Experimental Behavior 5. Kinetics in Solution a. Model for Rate of Denaturation b. Thermal Denaturation c. pH-Dependent Denaturation d. Urea Denaturation General ReferencesV. Limited Proteolysis and Aggregation in the Fibrinogen-Fibrin Conversion 1. The Relation to Blood Coagulation 2. Thrombin 3. Fibrinogen 4. General Aspects of the Thrombin-Fibrinogen Reaction 5. Step 1 a. Chemistry of Fibrinopeptides b. Kinetics of Step 1 c. Reversibility and Thermodynamics of Step 1 6. Step 2 a. Nature of the Intermediate Polymers b. Distribution Function for Intermediate Polymers c. Thermodynamics of Association 7. Step 3 General ReferenceVI. Some Experimental Methods 1. Introduction 2. Hydrodynamic, Thermodynamic, Optical, and Electrochemical Methods 3. Optical Rotation a. Experimental Quantities b. Status of Theory c. Rotatory Dispersion of Poly-γ-Benzyl-L-Glutamate d. Absolute Configuration of Amino Acids and Screw Sense of Helix e. Helical Content of Polypeptides f. Helix-Random Coil Transitions g. Protein Configuration 4. Deuterium-Hydrogen Exchange a. Effect of Deuterium-Hydrogen Substitution on Bond Strength b. Rate of Exchange in a Model Compound c. The Linderstrøm-Lang Method d. Theoretical Number of Exchangeable Hydrogen Atoms e. Theory f. Some Typical Results g. Discussion of Exchange Results 5. Infrared Absorption Spectra a. Characteristic Frequencies b. Dichroism c. Overtone and Combination Bands d. Deuterium Substitution 6. Ultraviolet Difference Spectra a. Origin of Difference Spectrum b. Charge Effects c. Medium Effects d. Hydrogen-Bonding Effects e. Discussion of Various Effects General ReferencesVII. Configurational Studies of Insulin, Lysozyme, and Ribonuclease 1. Insulin a. B26 Tyrosyl Residue b. B29 Lysyl Residue 2. Lysozyme a. Titration Curves b. Kinetics of Normalization of Carboxyl Groups c. Ultraviolet Difference Spectra 3. Ribonuclease a. Abnormal Carboxyl and Tyrosyl Groups b. Kinetics of Deuterium-Hydrogen Exchange c. Effect of Deuterium on the Transition Temperature d. Ultraviolet Difference Spectra and Optical Rotation e. A Model for Ribonuclease General ReferencesReferencesSubject Index