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Chemical Relaxation in Molecular Biology

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Table of Contents

Theory and Simulation of Chemical Relaxation Spectra.- I. Introduction.- A. The Relaxation Kinetic Progress Curve.- B. Optical Detection Signals.- C. Theoretical Description of Relaxation Kinetics.- D. Single Reaction Steps.- E. Approximations for Complex Reaction Systems.- F. Average Relaxation Times.- G. Computer Program for Simulation of Relaxation Spectra (FORTRAN IV).- 1. Numbering of Reacting Species.- 2. Numbering of Individual Reaction Steps.- References.- Concentration Correlation Analysis and Chemical Kinetics.- I. Introduction.- II. Properties of Thermodynamic Fluctuations.- A. Magnitude of Occupation Number Fluctuations.- B. Dissipation of Number Fluctuations.- III. Measurement of Number Fluctuations.- A. Fluorescence Correlation Analysis (FCA).- 1. Design of the FCA Experiment.- 2. Correlation Computers.- 3. Experimental Results.- B. Resistance Correlation Analysis (RCA).- C. Absorbance Correlation Analysis (ACA).- D. Quasi-Elastic Light Scattering (QELS) and Turbidity Correlation Analysis (TCA).- E. Orientation Correlation Analysis (OCA).- IV. Summary and Conclusions.- References.- Dynamics of Substitution at Metal Ions.- I. Introduction.- II. Formation of 1:1 Complexes with Small Ligands.- III. Formation of 1:1 Complexes with Large Ligands.- IV. The Effect of Bound Ligands.- A. Non-Ring Systems.- 1. Outer-Sphere Complex Formation.- 2. Labilisation of Remaining Water Molecules.- 3. Steric and Electronic Interaction Between Ligands.- 4. Coordination Number Change at the Metal.- B. Ring Systems.- V. Summary.- References.- Dynamics of Proton Transfer in Solution.- I. Introduction.- II. Theoretical Background of Proton Transfer.- A. Proton Affinities.- B. Stability of Hydrogen Bonded Molecular Complexes..- C. Potential Curves for Proton Transfer.- D. Dynamics of Proton Transfer in the Vapor Phase.- E. Gas Phase Solvation.- F. Theoretical Concepts and Mechanisms of Proton Transfer in Solution.- III. Proton Transfer in Aqueous Solution.- A. Intermolecular Proton Transfer.- B. Intramolecular Proton Transfer.- IV. Proton Transfer in Non-Aqueous Solvents.- A. Protic, Non-Aqueous Solvents.- B. Aprotic Solvents.- V. Biochemical Model Studies.- A. Amino Acids.- B. Purines and Pyrimidines.- 1. Formation of Hydrogen Bonded Complexes.- 2. Proton Transfer Reactions on Purines, Pyrimidines and Some Related Heterocyclic Compounds..- C. Coenzymes and Other Model Compounds.- D. Macromolecules.- VI. Polypeptides and Proteins.- A. Oligopeptides.- B. High Molecular Weight Polypeptides and Proteins..- VII. Experimental Techniques.- VIII. Conclusion.- IX. Other Review Articles and Books on Proton Transfer..- References.- Elementary Steps of Base Recognition and Hdlix-Coil Transitions in Nucleic Acids.- I. Introduction.- II. Elementary Steps of Bases Stacking.- A. Stacking of Monomer Bases and Hydrophobic Interactions.- B. Conformation Change of Single-Stranded Polynucleotides.- III. Ion Condensation to Polynucleotides.- IV. Recognition of Monomer Bases on a Polymer Template..- V. Helix-Coil Transition of Oligo(A)•Oligo(U).- A. Equilibrium Parameters According to the Cooperative Reaction Model.- B. Relaxation Data and Their Interpretation According to an “All or None” Model.- C. Unzippering at Helix Ends.- D. Chain Sliding.- VI. The Influence of GC Base Pairs.- VII. Specific Effects in Helix Loops.- VIII. Dynamics of Polymer Helix-Coil Transitions.- IX. Rate and Specificity of Genetic Information Transfer.- X. Summary.- References.- Structural Dynamics of tRNA. A Fluorescence Relaxation Study of tRNA.- I. Introduction.- II. Fluorescent Probes for the Structure of tRNA.- III. Pulsed Fluorescence Measurements.- A. The Lifetime of Excited States of the Fluorescent Probe and the Distribution of Conformational States.- B. Rotational Brownian Motion and Time-Dependent Fluorescence Anisotropy.- C. Instrumentation.- D. Results.- IV. Measurements Under Stationary Excitation.- V. Measurements of Chemical Rates.- A. Instrumentation and Data Evaluation.- B. Results.- VI. A Model for Aliosteric Conformations of tRNA.- A. Evaluation of the Parameters.- VII. Conformational States of tRNA with Regard to the Biological Role of tRNA.- References.- Chemical Relaxation Kinetic Studies of E. eoli RNA Polymerase Binding to Poly[d(A-T)] Using Ethidium Bromide as a Fluorescence Probe.- I. Introduction.- II. Experimental Procedures and Data Analysis.- A. Materials.- B. Fluorescence Temperature-Jump Measurements. Instrumentation and Conditions.- C. On-Line Computer Acquisition of Relaxation Data..- D. Analysis of Relaxation Curves by the Method of Modulating Functions.- III. Excluded Site Binding of Ethidium Bromide to Poly [d (A-T)].- A. Theory for the Equilibrium State.- B. Theory for Relaxation Kinetic Behavior.- C. Experimental Results and Analysis.- IV. Relaxation Kinetics of Ethidium Bromide and Poly [_d (A-T) J in the Presence of RNA Polymerase.- A. Experimental Conditions.- B. Experimental Results, Analysis, and Model Fitting.- V. Conclusions.- VI. Appendix. On the Derivation of General Equations for Relaxation Kinetics of Systems with Excluded Binding.- References.- Protein Folding and Unfolding.- I. Introduction.- II. Time-Independent Phenomena.- A. Van’t Hoff Analysis of Unfolding Reactions.- B. Recent Calorimetric Results.- III. “Slow” Temperature-Jump Methods.- A. Cells for Optical Measurements.- B. Cell for pH-Measurements.- C. Switching Unit and Thermostates.- D. Other Methods of Temperature Perturbation.- IV. Kinetics of Unfolding and Refolding.- A. Kinetic Difference Spectra.- B. Steady State Rates.- C. Transient Kinetics.- V. Theoretical Approach to the Kinetics of Folding.- A. Simple Sequential Model.- B. Lattice Model.- C. Isomerization Model.- D. Outline of a Phénoménologie Description.- E. Computer Simulation.- F. Outlook.- References.- Kinetics of Antibody-Hapten Interactions.- I. Introduction.- II. The Kinetics of the Association Step.- Concluding Remarks.- III. Kinetic Expression of the Elementary Interactions.- IV. Conformational Transitions Induced by Hapten Binding.- References.- Glutamate Dehydrogenase Self-Assembly. An Application of the Light Scattering Temperature-Jump Technique to the Study of Protein Aggregation.- I. Introduction.- II. Structural Features.- III. Thermodynamics of Self-Assembly.- A. Models.- B. Nonideality.- C. Nature of Interactions Between Oligomers.- D. Polymer Distribution.- IV. Scattered Light Detection in Chemical Relaxation Experiments.- A. Angular Dependence.- B. The Role of Virial Coefficients.- V. Kinetics of Self-Assembly.- A. The Sequential Model.- B. The Random Association Model.- C. Treatment of Kinetic Results.- D. Summary of Kinetic Results.- References.- Dynamic Aspects of Carrier-Mediated Cation Transport Through Membranes.- I. Introduction and General Considerations.- A. Biological Relevance.- B. Model Systems: Cation Selectivity of Antibiotics..- II. Kinetic Studies on Lipid Bilayer Membranes.- III. Elementary Steps Involved in Carrier-Mediated Cation Transport.- A. Elementary Steps Relevant to Proton Transport.- 1. Thermodynamic Parameters.- 2. Kinetics of Proton Transfer.- B. Elementary Steps Relevant to Alkali Ion Transport.- 1. Conformational Properties and Localization of Alkali Ion Specific Antibiotics in Membranes..- 2. Thermodynamic Aspects of Alkali Ion Specificity and Structure of Cation Complexes.- 3. The Kinetics and Mechanism of Complex Formation with Alkali Ions and Its Relevance to Cation Specificity.- IV. Comparison of the Dynamic Aspects of Cation Carriers Bound to Membranes and in Homogeneous Solution.- V. Summary.- References.
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