• Home
  • Textbooks
  • Physical Biology of the Cell
  • Dynamics of Molecular Motors

Physical Biology of the Cell

Rob Phillips, Jane Kondev, Julie Theriot

Chapter 16

Dynamics of Molecular Motors - all with Video Answers

Educators


Chapter Questions

03:36

Problem 1

An alternative definition for the randomness to that given in the chapter is
$$r=\lim _{t \rightarrow \infty} \frac{\left(x(t)^{2}\right)-(x(t))^{2}}{a(x(t))}$$
(a) Using the definition of randomness given above and the probability distribution for the one-state motor in the continuum limit, Equation $16.16,$ work out an explicit expression for the randomness.
(b) Equation 16.24 provides an expression for the randomness in terms of the force-dependent rate constants of one state of the model. Show that randomness in this
case is insensitive to whether the force dependence is in the forward or the backward rate. Make a plot of the randomness as a function of force. How does your result compare with the experimental curve shown in Figure $16.28(\mathrm{A}) ?$

Sana Riaz
Sana Riaz
Numerade Educator
03:20

Problem 2

single-molecule experiments have been performed on myosin V where a fluorescent marker was placed at different locations on the light-chain domain and individual steps were recorded. It was found that the average step size is about $37 \mathrm{nm}$; see Figure 16.53
(a) If the dye is placed on the light-chain domain at a distance $x$ along the direction of motion from the midpoint between the two heads of the motor, what step size do you expect to observe? What value of $x$ explains the data shown in Figure $16.53 ?$ What do you suppose is the origin of the peak at approximately $74 \mathrm{nm}$ in the step-size histogram?
(b) Assume that the stepping rate is $k$. This is the probability per unit time that the motor will make a step. Calculate the waiting time distribution between the two steps observed in the experiment if the fluorescent marker is placed at position $x$ found in (a). What is the expected distribution, assuming a hand-over-hand stepping mechanism if the marker is placed very close to one of the heads (that is, $x=18 \mathrm{nm}$ )? Üse your calculated distributions to rationalize and fit the data (from Yildiz et al., 2003 ) provided on the book's website. Does your analysis support the hand-over-hand mechanism? What value of $k$ do you obtain?

Sana Riaz
Sana Riaz
Numerade Educator
04:00

Problem 3

As described in the chapter, careful measurements have been performed that examine the dependence of motor velocity on ATP concentration. Under certain conditions, the hydrolysis reaction performed by a molecular motor can be described using the Michaelis-Menten model introduced in Section $15.2 .7(\mathrm{p} .596) .$ In the particular case of kinesin, its stepping is strongly coupled to its ATPase activity, which translates into relatively constant step sizes. Finally, its high processivity allows for a clear definition of a speed, since kinesin takes many steps before falling off the microtubule.
Relate the reaction speed (the rate of ATP hydrolysis) to the maximum stepping speed of kinesin and determine its dependence on ATP concentration. Fit your model to the data by Schnitzer and Block (1997) shown in Figure 16.54 and provided on the book's website. Then work out what change in substrate concentration is needed to increase the reaction rate from $0.1 \mathrm{v}_{\max }$ to $0.9 \mathrm{V}_{\max }$

Sana Riaz
Sana Riaz
Numerade Educator
02:22

Problem 4

In the chapter, in order to obtain the velocity of a two-state motor, we made use of a trick to circumvent solving the master equation directly. Here we take up this task and in the process also derive an expression for the diffusion constant.
(a) Consider a trial solution of the system of equations for $p_{0}(n, t)$ and $p_{1}(n, t),$ given by Equations 16.33 and 16.34
Find a relation between $K$ and $\omega$ that guarantees the existence of a solution of this form. This is the so-called dispersion relation.
(b) By substituting the trial solution $\mathrm{e}^{\mathrm{i}[(K / a)-\omega t]}$ into the differential equation for diffusion with drift (Equation 13.54 ,
p. 530 , show that the dispersion relation in this case is
$$\omega=v \frac{K}{a}-i D \frac{K^{2}}{a^{2}}$$
where $v$ is the drift velocity and $D$ is the diffusion constant.
(c) Demonstrate that in the limit $K \ll 1$, the dispersion relation for the two-state motor is the same as that for diffusion with drift. To do this, Taylor-expand $\omega(K)$ in $K$ and solve the equation for $\omega$ obtained in (a) order by order in $K$ which amounts to computing the coefficients in the Taylor expansion. Compare your result with the dispersion relation for dispersion with drift and read off the diffusion coefficient for the motor and its speed. Check that the formula for the speed matches the one obtained in the chapter.

Sana Riaz
Sana Riaz
Numerade Educator
02:16

Problem 5

In the chapter, we analyzed the polymerization ratchet in the two limiting cases of diffusion-limited and reaction-limited polymerization. By comparing the time for a load, a polystyrene sphere 1 y $m$ in diameter, to diffuse a distance given by the actin monomer size, and the average time for an actin monomer to be added to the growing end of the filament, find the condition for the free actin monomer concentration that is necessary for the polymerization in the presence of the load to be reaction-limited. Compare this concentration with the critical concentration for actin filament growth.

Sana Riaz
Sana Riaz
Numerade Educator