El. knyga: Data Analysis in Biochemistry and Biophysics

ForewordPreface Acknowledgments1. Scope of Problems Investigated
1. Introduction
2. A Problem from Absorption Spectroscopy
3. The Use of Function Minimization and Matrices
4. An Example from
Concentration-Dependent Aggregating Systems
5. Linear and Nonlinear
Models
6. The General Problem for Linear Models
7. The
General Problem for Nonlinear Models
8. The Use of Statistics
9. The Problem of Constraining the Parameters
10. Determining
Unknown Components: Matrix Rank Analysis
11. A Word of Caution
References2. Matrices
1. Introduction
2. Matrices
3. Rules of Matrix Algebra
4. Special Matrices
5.
Determinants of Square Matrices
6. Matrix Rank and Elementary
Transformations
7. The Inverse of a Matrix
8. Vector
Algebra
9. Linear Equations
10. Quadratic Forms
11. Eigenvalues and Eigenvectors
12. Partitioned Matrices
13. Application to Coordinate Geometry and Bilinear Forms
References3. Analysis Pure Analysis
1. Sets
2.
Functions and Their Properties
3. Functions of Several Real
Variables Applied Analysis
4. Applications of Differentiation
5. Applications of Integration
6. Miscellaneous Topics
References4. Minimization of Functions
1. Introduction
2.
Functional Extrema
3. Least Squares
4. Minimax Curve
Fitting or Chebyshev Minimization
5. Linear Programming
6.
Determination of Parameters in Nonlinear Models
7. Application
References5. Statistics I
1. Introduction
2. Sample
Space and Elementary Consideration of Probability Distributions
3.
Frequency Distributions
4. Probability
5. Standard
Distributions with a Single Variable
6. Bivariate Distribution
7. Multivariate Distributions
8. Statistical Inference
9. Distributions of Quadratic Forms References6. Statistics II
1. Introduction
2. Hypothesis Testing
3. Formalizing
Notions on Hypothesis Testing
4. The General Linear Model of Full
Rank
5. Testing General Linear Model Hypotheses
6. Some
Notes on Nonlinear Models References7. Absorption Spectra of
Mixtures
1. Introduction
2. Absorption Spectra of Mixtures
3. Applications in Protein Modification to Determine Reactivity of
Amino Acid Residues
4. Application to Solvent Perturbation
5. Binding Studies References8. Analysis of Nucleic Acid Spectra
1. Introduction
2. RNA Spectra
3. DNA Spectra
References9. Matrix Rank Analysis
1. Introduction
2. The
Matrix Rank Analysis Method
3. Application of Matrix Rank Analysis
to the Optical Rotatory Dispersion Spectra of TMV RNA Taken at a Variety of
Ionic Strengths and Temperatures
4. Application to Reaction Rates of
Partially Oxidized Hemoglobin
5. Alternative Methods for Determining
the Shape of the Spectra References10. Optical Rotary Dispersion and
Circular Dichroism of Proteins
1. Introduction
2. Possible
Structures of Proteins and Polypeptides (the Ramachandran Diagrams)
3. Methods for Determining the Secondary Structure of Proteins
4.
Problems Involved in Optical Rotatory Dispersion Analysis of Proteins
5. Possible Methods for Determination of Side Chain Contributions
6. Circular Dichroism of Proteins
7. Fitting an Optical Rotatory
Dispersion Curve with Drude Terms
8. Analysis of Circular Dichroism
Spectra
9. Decomposition of Optical Rotatory Dispersion Curves into
Their Contributing Circular Dichroic Bands References11. Optical
Rotatory Dispersion and Circular Dichroism of Nucleic Acids and their
Components
1. Introduction
2. ORD of RNA Components
3. Possible Sequence Determination and Distinguishing between Isomers
4. Calculation of ORD of Homopolymers and RNA
5. Testing
Hypotheses about RNA Structure
6. Optical Rotatory Dispersion of RNA
References12. Aggregating Systems
1. Introduction
2. Aggregation Schemes
3. Number Average Molecular Weights: Ideal
Systems
4. Weight Average Molecular Weights
5. Gel
Filtration Methods in the Determination of Molecular Weight Distributions
6. Mixed Aggregation References13. Allosteric Effects and Other
Cooperative Phenomena in Protein-Ligand Equilibria
1. Introduction
2. Description of Some Models in the Literature
3. Sequential
Binding or Adair's Equation-Proteins without Any Subunits
4. Models
of Koshland, Nemethy, and Filmer
5. The Model of Monod, Wyman, and
Changeux
6. Expansion of Models
7. Cases Considered by
Frieden
8. Scatchard's Model
9. Distinguishing between
Different Models
10. Comments on Procedures
11. Analysis of
Data References14. Enzyme Kinetics
1. Introduction
2. Two Cases Treated by Wilkinson
3. The Effects of pH on Vmax
4. Cases Treated by Cleland
5. A Complex Case and Ways of
Handling It References15. Rapid Reactions: Transient Enzyme Kinetics
and Other Rapid Biological Reactions
1. Introduction
2.
Techniques of Measuring Rapid Reactions
3. Combination of Hemoglobin
with Ligands
4. A Potential Method for the Determination of Spectra
of Intermediates
5. Determination of the Number of Intermediates and
Rate Constants in Enzyme Catalyzed Reactions
6. Relaxation Methods
7. A Word of Caution References16. Tracer Techniques in
Compartmentalized Systems
1. Introduction
2.
Two-Compartment Systems
3. Closed Systems and Open Systems
4. Three-Compartment Systems
5. Problems with the Use of
Simultaneous Linear Differential Equations
6. Multicompartment
Systems
7. Simulation of Tracer Data
8. Modification of the
Multicompartment System Model and Other Models ReferencesAppendix:
Statistical TablesAuthor IndexSubject Index