Energy Coupling and Molecular Motors

This volume examines a number of different molecular motors that utilize ATP. The molecular machines to be discussed include ATP synthase, myosin, kinesin, DNA helicases, DNA topoisomerases, chaperones and bacterial rotory motors. The discussion of these various molecular motors is rarely undertaken in one volume and will serve as a great resource for scientists studying structure and function of multiprotein complexes as well as those working on energy coupling mechanisms. The areas of research presented in this volume do not normally overlap, and yet they share common mechanisms. This volume examines a number of different molecular motors that utilize ATP. The molecular machines to be discussed include ATP synthase, myosin, kinesin, DNA helicases, DNA topoisomerases, chaperones and bacterial rotory motors. The discussion of these various molecular motors is rarely undertaken in one volume and will serve as a great resource for scientists studying structure and function of multiprotein complexes as well as those working on energy coupling mechanisms. The areas of research presented in this volume do not normally overlap, and yet they share common mechanisms.

Preface

xi

1. Muscle Contraction

YALE E. GOLDMAN

I.Introduction

2

(1)

II. Sarcomere Structure

3

(4)

III. Distribution of Myosin Superfamily Members and Contractile Proteins

7

(1)

IV. Myosin Structure

8

(4)

V. Working Hypothesis

12

(3)

VI. Actomyosin ATPase Cycle in Solution

15

(5)

VII. Comparison of ATPase Kinetics Between a Protein Suspension and the Sarcomeric Filament Lattice

20

(1)

VIII. Myofibrillar ATPase

21

(1)

IX. Muscle Fiber Mechanics and Energetics

22

(6)

X. Biochemical Rate Constants in Muscle Fibers

28

(5)

XI. Structural Changes Leading to Force Generation and Filament Sliding

33

(9)

XII. Why Does Myosin Have Two Heads?

42

(1)

XIII. Summary, Uncertainties and Future Directions

43

(2)

References

45

(10)

2. Mechanics of Unconventional Myosins

RONALD S. ROCK, THOMAS J. PURCELL, AND JAMES A. SPUDICH

I. Introduction

55

(2)

II. Single-Molecule Analysis Revealed a Unitary Small Step in Motion as Myosin Interacts with Actin

57

(2)

III. Molecular Genetic Approaches have Indicated Roles of Various Domains and Specific Residues of the Myosin Motor

59

(2)

IV. The Unconventional Myosins V and VI are Adapted for Cellular Transport Roles

61

(3)

V. Requirements of Processive Motors

64

(18)

VI. Conclusions and Perspectives

82

(1)

References

83

(5)

3. Motor Proteins of the Kinesin Superfamily

DAVID D. HACKNEY

I.Introduction

88

(2)

II. Structure

90

(11)

III. Characterization of Motility

101

(6)

IV. ATPase Mechanism

107

(10)

V. MT Decoration

117

(3)

VI. Generation of Motility

120

(13)

VII. Regulation and Cargo Binding

133

(3)

VIII. Perspectives

136

(1)

References

137

(7)

4. The Bacterial Rotary Motor

HOWARD C. BERG

I.Introduction

144

(1)

II. Bacterial Behavior

145

(6)

III. The Flagellar Motor

151

(33)

IV. Future Work

184

(1)

References

185

(19)

5. The ATP Synthase: Parts and Properties of a Rotary Motor

THOMAS M. DUNCAN

I. Overview

204

(1)

II. Conservation of General Structure and Function in F0F1

205

(3)

III. The Binding-change Mechanism for ATP Synthesis and Hydrolysis

208

(2)

IV. F,'s Structural compatibility with a Cooperative, Rotary Mechanism

210

(6)

V. Demonstration and Analysis of Subunit Rotation in Fi and in F0F1

216

(19)

VI. Further Characteristics of Fo and F1 Subunits as Components of the Rotor or Stator

235

(27)

VII. Remaining Puzzles for Rotational Catalysis

262

(3)

References

265

(12)

6. Bacteriophage T7 Gene 4 Protein: A Hexameric DNA Helicase

DONALD J. CRAMPTON AND CHARLES C. RICHARDSON

I.Introduction

277

(4)

II. Isolation and Characterization

281

(2)

III. Structural and Biochemical Properties

283

(7)

IV. Models for Energy Transduction

290

(8)

V. Future Directions

298

(1)

References

299

(5)

7. DNA Helcases, Motors that Move Along Nucleic Acids: Lessons from the SF1 Helicale Superfamily

TIMOTHY M. LOHMAN, JOHN HSIEH, NASIB K. MALUF, WEA CHENG, AARON L. LUCIUS, CHRISTOPHER J. FISCHER, KATHERINE M. BRENDZA, SERGEY KOROLEV, AND GABRIEL WAKSMAN

I.Introduction

304

(3)

II. Phenomenological Features of DNA Unwinding

307

(2)

III. Structural Features of SF! DNA Helicases

309

(11)

IV. Protein Oligomerization

320

(3)

V. DNA Binding by E. coli Rep

323

(6)

VI. Mechanisms of Nucleotide Binding and ATP Hydrolysis by E. coli Rep

329

(4)

VII. Single-Stranded DNA Translocation by Monomers of SF1 Helicases

333

(3)

VIII. Presteady-State, Single-Turnover DNA Unwinding Studies

336

(3)

IX. DNA Unwinding by E. coli Rep and UvrD Helicases

339

(9)

X. Helicale Activity of SF! Monomers

348

(2)

XI. E. coli RecBCD Helicale

350

(4)

XII. Proposed Mechanisms for DNA Unwinding and Translocation by SF1 Helicases

354

(8)

XIII. Summary

362

(2)

References

364

(8)

8. Type II DNA Topoisomerases: Coupling Directional DNA Transport to ATP Hydrolysis

JANET E. LINDSLEY

I.Introduction

372

(2)

II. Basic Biochemical and Structural Information about Type II Topoisomerases

374

(6)

III. The Mechanism of Strand Passage

380

(13)

IV. Concluding Thoughts

393

(1)

References

394

(6)

9. The Role of ATP in Directing Chaperonin-Mediated Polypeptide Folding

ARTHUR L. HORWICH AND WAYNE A. FENTON

I. The Work Carried out by Chaperonins

400

(2)

II. ATP Action in Driving Chaperonin-Assisted Protein Folding - Structural States and the Overall Chaperonin Cycle

402

(9)

III. Mechanistic Studies of the Nucleotide Cycle

411

(5)

IV. Polypeptide and the Nucleotide Cycle

416

(5)

V. Cooperativity and Allostery

421

(9)

References

430

(5)

Author Index

435

(34)

Subject Index

469

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