Proteins : Analysis and Design

Proteins: Analysis and Design focuses solely on individual experimental approaches, rather than on specific classes of proteins. The book provides insight into the important issues in protein science and how one can cope with them. These include all issues which explore the detailed relationship of protein structure to function.

Dedication

v

(4)

Contributors

ix

(2)

Preface

xi

Introduction

1

(3)

Ruth Hogue Angeletti

Chapter 1 Current Problems and Technical Solutions in Protein Biochemistry

4

(117)

Ruedi Aebersold

Scott D. Patterson

I. Introduction

4

(2)

II. Early Events in Signaling by Interferons: From Membrane Receptor to Induced Genes

6

(2)

III. Detection of Systems Components

8

(9)

IV. Identification of Components of Complex Systems

17

(33)

V. Analysis of Regulatory Modifications of Components of Complex Systems

50

(26)

VI. Analysis of Protein: Ligand Complexes

76

(17)

VII. Conclusion

93

(1)

References

94

(27)

Chapter 2 Posttranslational Modifications

121

(87)

Radha Gudepu Krishna

Finn Wold

I. Introduction

121

(4)

II. Types of Posttranslational Derivatives

125

(34)

III. Types of Posttranslational Reactions: How Modifications Are Made

159

(16)

IV. Biological Functions of Posttranslational Modifications: Why Modifications Are Made

175

(17)

References

192

(16)

Chapter 3 Design and Use of Synthetic Peptides as Biological Models

208

(51)

Janelle L. Lauer

Gregg B. Fields

I. Peptides as Structural Models of Proteins

208

(11)

II. Cell/Peptide Interactions

219

(9)

III. Protein/Peptide Interactions

228

(8)

IV. Peptides and Modulation of T-Cell Behavior

236

(4)

V. Enzyme/Peptide Interactions: Peptides as Enzyme Substrates

240

(3)

VI. Summary

243

(1)

References

243

(16)

Chapter 4 Site-Directed Mutagenesis and Protein Engineering

259

(54)

Gary S. Coombs

David R. Corey

I. Introduction

259

(1)

II. Why Alter Proteins?

260

(1)

III. Techniques for Oligonucleotide-Directed Mutagenesis

261

(11)

IV. Strategies for Engineering Proteins

272

(19)

V. Case Studies: Introduction of Function by Site-Directed Mutagenesis

291

(11)

VI. Conclusion

302

(1)

References

303

(10)

Chapter 5 De Novo Design of Protein Structure and Function

313

(42)

Michael W. Klemba

Mary Munson

Lynne Regan

I. Introduction and Overview

313

(1)

II. De Novo Design of Structure

314

(5)

III. Characterizing the Design

319

(1)

IV. Selected Examples of Designed Proteins

320

(11)

V. De Novo Design of Function

331

(13)

VI. Design of Catalytic Proteins

344

(4)

VII. Summary and Future Directions

348

(1)

References

348

(7)

Index

355

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Proteins : Analysis and Design

Summary

Table of Contents

Supplemental Materials