Mechanics of
Motor Proteins and the Cytoskeleton
by Jonathon Howard
Contents (partly abridged)
1 Introduction
|
|
| PART I PHYSICAL
PRINCIPLES |
| |
2 Mechanical
Forces
Force; single-molecule level
Motion of Springs, Dashpots, and Masses Induced by Applied Forces ; |
|
bacterial motor |
| Motion of Combinations
of Mechanical Elements; bacterial inertia, proteins, |
|
chemical bonds |
Motion of a Mass
and Spring with Damping; motor proteins
Work, Energy, and Heat; chemical bonds, protein conformations
Summary: Generalizations to More Complex Mechanical Systems |
|
Problems |
| |
3 Mass, Stiffness,
and Damping of Proteins
Mass; Elasticity; tension rod, springs
The Molecular Basis of Elasticity; solids
Viscous Damping; jar of honey
The Molecular Basis of Viscosity
The Global Motions of Proteins are Overdamped; ribosome
The Motions of the Cytoskeleton and Cells Are Also Overdamped
Summary; Problems |
|
|
4 Thermal Forces
and Diffusion
Boltzmann's Law; applications
Equipartition of Energy
Diffusion as a Random Walk
Einstein Relation; diffusion of ions
Some Solutions to the Diffusion Equation; Point Source; First-Passage Times
Correlation Times*; free and tethered proteins
Fourier Analysis*; power spectrum
The Magnitude of the Thermal Force*; electrical circuits
Summary; Problems
*An asterisk denotes a more advanced section. |
|
|
5 Chemical Forces
Chemical Equilibria
The Effect of Force on Chemical Equilibria; ion channels in hair cells
Rate Theories of Chemical Reactions
Effect of Force on Chemical Rate Constants; ratchet models for motor proteins; |
|
unfolding titin
|
| Bimolecular Reactions:
association rates; Michaelis-Menten equation; |
|
protein complexes
|
Cyclic Reactions
and Free Energy Transduction
Summary; Problems |
|
|
6 Polymer Mechanics
Flexural Rigidity and the Beam Equation
Applications of the Beam Equation: Bending and Buckling; cantilever, glass |
|
fibers; microtubules,
coiled coil; buckling; force required for a microtubule |
Drag Forces on Slender
Rods; sperm; gliding assays
Dynamics of Bending and Buckling; relaxation of MTs and action filaments; |
|
time constant of
a force fiber |
| Thermal Bending
of Filaments: persistence length, semiflexible polymers, |
|
entropic elasticity,
spring constant of a freely jointed chain, worm-like chain |
| Summary |
|
|
| PART II CYTOSKELETON
7 Structures of Cytoskeletal
Filaments
Structures of the Subunits
Families of Cytoskeletal Proteins: Actin, Tubulin,
|
|
Intermediate Filament
Proteins |
| Filament Structures:
Actin Filament, Microtubule, Coiled Coils, |
|
Intermediate Filaments |
| Summary: Structural
Basis for the Length, Strength, Straightness, and Polarity |
|
of Filaments |
| |
|
8 Mechanics of
the Cytoskeleton
Rigidity of Filaments in Vivo: Actin in Muscle, in Sterocilia, Microtubules
in |
|
Sperm, Keratin-Containing
Materials |
| Rigidity of Filaments
in Vitro: Actin, Microtubules, Coiled Coils, |
|
Intermediate Filaments,
Bacterial Flagella, DNA and Titin |
| Summary: Material
Properties of Cytoskeletal Proteins |
|
|
9
Polymerization of Cytoskeletal Filaments
Passive Polymerization: The Equilibrium Polymer
Single-Stranded Filaments Are Short
Multistranded Filaments Grow and Shrink at Their Ends
Other Properties of Multistranded Filaments
Binding Energies and the Loss of Entropy
Structure and Dimensionality
Summary; Problems
|
10 Force Generation
by Cytoskeletal Filaments
Generation of force by Polymerization and Depolymerization in Vivo
Generation of Force in Vitro
Equilibrium Force
Brownian Ratchet Model: Reaction-Limited Polymerization, Diffusion-Limited |
|
Polymerization |
| Examples of Motility
Driven by Actin Polymerization; listeria, in |
|
sea cucumber sperm |
| Other Kinetic Models;
Summary |
|
|
11 Active Polymerization
Actin and Tubulin Hydrolysis Cycles
Filament Polarity, Treadmilling, and Nucleation
Dynamic Instability; switching between growth and shrinkage, GTP-cap model
Work during Polymerization and Depolymerization
Structural Changes Attending Nucleotide Hydrolysis
Summary
PART III Motor Proteins
12 Structures of Motor Proteins
Crossbridges and the Domain Organization of Motor Proteins
Motor Families
High-Resolution Structures
Docking of Motors to Their Filaments
Summary
13 Speeds of Motors
The Speeds of Motors in Vivo
Rowers and Porters
In Vitro Motility Assays
Processive and Nonprocessive Motors
The Hydrolysis Cycle and the Duty Ratio
Analogies to Internal Combustion Machines and Animal Locomotion
Summary: Adaptation to Function
|
|
|
14 ATP Hydrolysis
ATP: adenosine triphosphate
Coupling Chemical Changes to Conformational Changes
Hydrolysis of ATP by Skeletal Muscle Mysosin: Without and with action
Hydrolysis of ATP by Conventional Kinesin: Without and with microtubles;
|
|
head coordination. |
| Functional Differences
between Kinesin and Myosin ATPase Cycles: Kinesin is |
|
attached during
its rate limiting step, but myosin is detached;
Biochemical evidence for kinesin's processivity, that Mysosin has a low
duty ratio |
| Summary |
|
|
15 Steps and
Forces
Distances that Characterize a Motor Reaction
Single-Motor Techniques: forces; displacements; sensitivity of a |
|
photodetector; calibration,
single-molecule fluorescence |
Steps, Paths, and
Force: Conventional Kinesin; Myosin II; Other Motors
The Structural Basis for the Duty Ratio
Summary |
|
|
16 Motility Models:
From Crossbridges to Motion
Macroscopic and Microscopic Descriptions of Motility
Powerstroke Model
Role of Thermal Fluctuations in the Power Stroke
Crossbridge Model for Muscle Contraction
Comparison of the Model to Muscle Data: Force-Velocity Curve and Efficiency; |
|
Transients;
Powerstroke, Path Distance and Duty Ratio; One step per ATP |
| A Crossbridge Model
for Kinesin |
| Summary: Comparison
between Motile Systems
Afterword
Appendices: (see selected
contents list below)
Bibliography
Index
|