Analytical molecular biology / by Tai Te Wu.

Format:

Book

Author/Creator:

Wu, Tai Te, 1935-

Language:

English

Subjects (All):

Molecular biology--Mathematics.

Molecular biology.

Computational Biology.

Medical Subjects:

Computational Biology.

Physical Description:

xiii, 258 pages : illustrations ; 25 cm

Place of Publication:

Boston : Kluwer Academic Publishers, [2001]

Summary:

Analytical Molecular Biology illustrates the importance of simple analytical methods applied to some basic molecular biology problems, with an emphasis on the importance of biological problems, rather than the complexity of mathematics. First, the book examines crucial experimental data for a specific problem. Mathematical models will then be constructed with explicit inclusion of biological facts. From such models, predictions can be deduced and then suggest further experimental studies. A few important molecular biology problems will be discussed in the order of the complexity of the mathematical models. Based on such illustrations, the readers can then develop their own analytical methods to study their own problems. This book is for anyone who knows they need to learn how to apply mathematical models to biology, but doesn't necessarily want to, from practicing researchers looking to acquire more analytical tools to advanced students seeking a clear, explanatory text.

Contents:

Chapter 1. Antibodies binding antigens 1

Beginning of immunochemistry 2

Verification of predictions 12

Switch peptide and J-minigene 14

Uniqueness of CDRH3 18

Coding of CDRH3 20

Vaccination 23

Chimeric antibodies 24

Humanizing mouse antibodies 25

Human antibodies in mouse 27

Phage display library 27

Folding of CDR's and prediction of antibody combining sites 28

Antibody design 28

Application to other problems in molecular biology 28

Chapter 2. Saturation of hemoglobin with oxygen at equilibrium 37

Structures of myoglobin and hemoglobin 38

Equilibrium binding of myoglobin with oxygen 40

Experimental measurements of saturation of hemoglobin with Oxygen at equilibrium 43

One-constant model 45

Two-constant model 47

Three-constant model 51

Least square fitting 55

Prediction based on these constants 58

Further experimental studies 59

Other studies on hemoglobin 62

2,3-Diphosphoglycerate 62

Other allosteric proteins and enzymes 62

Chapter 3. Co-transduction and location of Escherichia coli Genetic markers 65

Conjugation 66

Transduction 67

Model for random generalized transduction 70

Three-point analysis 74

An example 80

Escherichia coli genetic map 85

Future work 87

Chapter 4. Enzyme kinetics 91

Simplified reaction 92

Rate equations 93

Simple enzyme kinetics 94

Transition region 100

Low substrate concentration 103

Numerical solution for non-linear rate equations 108

Inhibitors 110

Future studies 115

Chapter 5. The [phi] and [psi] angles of proteins 117

The [phi] and [psi] angles 118

Precise definition of the [phi] angle 120

Precise definition of the [psi] angle 121

Protein data bank 122

Unit normals to planes 123

[phi] and [psi] angles as angles between planes 123

An example 124

Bond distances and bond angles 128

Ramachandran ([phi],[psi]) plot and steric hindrance 129

Allowed configurations of amino acid residues 132

Calculations of coordinates of non-bonding atoms 135

Other interaction potentials between non-bounded atoms 139

Distance between nearest neighboring C[subscript a] atoms 141

Secondary structures of polypeptides 142

Chapter 6. Prediction of protein folding 145

Reference proteins 147

Selecting [phi] and [psi] 149

Backbone structure predictions 152

Side chain structure prediction 167

Future theoretical structural studies 173

Chapter 7. Structures of polynucleotides 177

Periodic structures 178

Glycosidic bond 179

Five degrees of freedom of the backbone 182

Ribose ring structure 190

Virtual angles 191

Future analysis 191

Chapter 8. Fiber X-ray diffraction and DNA double helix 193

Some simple properties of J[subscript n] 194

X-ray diffraction pattern of helical line 198

Diffraction patterns of combination of helices 204

Biological consequences of DNA double helix 207

An alternative helical structure of DNA 209

Possible biological implications 213

Future experiments 215

Logarithm 222

Simultaneous linear algebraic equations 223

Quadratic algebraic equation 224

Translation and rotation of Cartesian coordinates 225

Derivative 228

Integration 230

Vectors 231

Simple differential equation 233

Complex variable 234

Fourier transform 236.

Notes:

Includes bibliographical references and indexes.

ISBN:

0792374479

OCLC:

47073032