# Modelling Molecular Motors as Folding-Unfolding Cycles

## Abstract

We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response. The main improvement with respect to previous models is that this description suggests a connection between folding and function of allosteric proteins.

An important class of proteins are alosteric: part of the molecule undergoes large conformational changes as a result of a chemical reaction which takes place in another region of the protein. One example of this is motor proteins which through a series of conformational changes perform directed motion using the chemical energy gained $`ATP`$ hydrolysis. Physicists have proposed that this may be viewed as a ratchet-like mechanism, similar to Feynman’s famous ratchet  but with the addition that ATP binding/hydrolysis has the ability to turn this ratchet on and off. Several models have been proposed along this lines, see .

The energy associated with the chemical cycle of real motor proteins is comparable to the total binding energy of a protein. This leads us to speculate that the directed motion associated to motor action may be connected to the pathway for protein folding. Thus, we propose to describe the motor variables in terms of a pathway parametrization of protein folding  using three variables $`\phi _0`$, $`\phi _1`$ and $`\phi _2`$, that each takes value $`0`$ or $`1`$. These variables, which label the conformations visited during the motor cycle, also label subsequent states along the folding pathway of the protein. Thus we propose that the energy function of the motor protein in the absence of ATP and external load is described by the Hamiltonian :

$$H_0=\phi _0\phi _0\phi _1\phi _0\phi _1\phi _2.$$
(1)   
The ground state of $`H_0`$ is $`(\phi _0,\phi _1,\phi _2)=(1,1,1)`$. At low temperatures $`T`$ the variables will tend to freeze into the ground state, whereas they melts for $`T>T_c=1/\mathrm{ln}(2)`$. In order to take into account ATP hydrolysis and an external load we suggest the following extension of the energy function:

$$H_1=[ATP]\phi _0\phi _0\phi _0\phi _1\phi _0\phi _1\phi _2+F(\phi _0,\phi _1,\phi _2)$$
(2)   
where \[ATP\] represents the effects of ATP on the chemical potential of the molecule. \[ATP\] can cycle between two values, say $`0`$ and $`A`$ where $`A`$ is the energy associated to hydrolysis, and $`F`$ is the external load on the motor. With this structure we single out one variable $`\phi _0`$ to represent ATP binding and hydrolysis while the two other variables represent events associated to attachment ($`\phi _1`$) and mechanical motion ($`\phi _2`$) of the motor.

The dynamics of the motor is generated by switching ATP between $`A`$ and $`0`$. When ATP is zero, $`\phi _0`$ is driven to $`\phi _0=1`$ by the first term in the energy function. Subsequently this sets an ordering where typically first the variable $`\phi _1`$, then the variable $`\phi _2`$ takes the value $`1`$. Thus first the “leg” binds to the substrate, then it performs a step (or “power stroke”) $`\phi _2=01`$, and it advances forward by one step. In case it by chance do the opposite, i.e. if $`\phi _2`$ moves before $`\phi _1`$ it represent the event when the stroke takes place before the binding, and we assign it a one step backwards movement. When $`(\phi _1,\phi _2)=(1,1)`$ we initiate the chemical switch \[ATP\] $`=0A`$ which subsequently forces $`\phi _00`$, and accordingly release the binding constraints of $`\phi _1,\phi _2`$. The ordering of the melting of these variables is random. The asymmetry in the freezing — where the process typically proceed in the order $`\phi _01`$, $`\phi _11`$ and $`\phi _21`$ — and the melting — which can proceed in any order, we refer to as the mirror effect , and lies at the heart of the functioning of this motor. The total move table is

$`(\phi _1,\phi _2)`$ $`=`$ $`(0,0)(1,0)(1,1)\text{defines move}xx+dx`$ (3)   
$`(\phi _1,\phi _2)`$ $`=`$ $`(0,0)(0,1)(1,1)\text{defines move}xxdx`$ (4)   
$`(\phi _1,\phi _2)`$ $`=`$ $`(1,1)(1,0)(0,0)\text{defines move}xxdx`$ (5)   
$`(\phi _1,\phi _2)`$ $`=`$ $`(1,1)(0,1)(0,0)\text{defines move}xx+dx`$ (6)   
In terms of the normal nomenclature in the literature on motor molecules, the moves of Eq.(3) represent respectively the binding and the working stroke whereas the moves in Eq. (5) undo these. The moves of Eq. (6) then represent the optimal sequence of unbinding and recovery.

In order to study the model numerically, we have chosen to use the following dynamics: In each update, either zero or one of the $`\phi `$-variables changes value. The probability that a given change is made (either $`(\phi _0,\phi _1,\phi _2)(1\phi _0,\phi _1,\phi _2)`$, $`(\phi _0,1\phi _1,\phi _2)`$, $`(\phi _0,\phi _1,1\phi _2)`$, or $`(\phi _0,\phi _1,\phi _2)`$) is proportional to the Boltzmann factor associated with the configuration the model is entering into,

$$P(s_is_f)e^{H_1(s_f)/T}.$$
(7)   
where $`s_i`$ and $`s_f`$ are initial and final states respectively. As the variables are discrete, it is not possible to assign a physical time to the process. However, the amount of ATP that is hydrolyzed (i.e., the number of times $`A`$ takes the value $`a`$) is a natural clock in this process.

A more realistic dynamics for this model is based on constructing a Langevin equation from the Hamiltonian (2). Continuous variables may then be used and a connection with “real time” may be made. The Langevin equation reads

$$\frac{d\phi _i}{dt}=\mu _i\frac{dH_1}{d\phi _i}+\eta _i(t)$$
(8)   
where $`\mu _i`$ are mobilities, $`\eta _i(t)`$ thermal noise and the variables $`\phi _i`$ now has to be continuously varying . To obtain the real cycle times we in addition have to introduce the residence times in the different states. We note that if the limiting step of the dynamics is the ATP binding, i.e. at very low ATP concentration, then the efficiency curves given by the phase space method also represent real time velocity curves up to timescale that is given by ATP hydrolysis rate. In the opposite limit, the Langevin dynamics captures the timescale of the motion through the coefficients $`\mu _i`$. Experiments show a roughly linear load-velocity characteristics . We can obtain a linear dependence with this Langevin dynamics for certain realizations of the force but this feature appears not to be robust with respect to the functional form of the load.

In Figure 1 we show the average position of the motor as function of the number of times an ATP molecule was hydrolyzed, i.e., that the ATP was switched from $`0`$ to $`A`$. In the figure we show two cases, both for $`A=4`$, one at a low temperature $`T=0.25`$ (the upper curve) and one at a high temperature, $`T=5`$. In each case the corresponding mean trajectories are also shown (average over 5000 trajectories). First we note the high efficiency, for the $`T=0.25`$ case. About 95% of the hydrolysis events lead to forward motion. Such a high efficiency is seen in real motor proteins at least at low ATP concentrations .

Coming back to the drag force we note that its form has to fulfill certain conditions. Firstly it should act through pushing the system into a particular “corner” of configuration space. Secondly, the drag force should not change the ATP parameter $`A`$ directly. However, the reaction rate, set by the term $`[\text{ATP}]\phi _0`$, can be influenced through forcing the dynamical variables $`\phi _0`$, $`\phi _1`$ and $`\phi _2`$. Thirdly, the drag force influences the motor function through changing the rate of entering the state $`(\phi _1,\phi _2)=(1,1)(0,0)`$ vs. the $`(\phi _1,\phi _2)=(0,0)(1,1)`$ rate. An explicit realization that fulfills these conditions are

$$F(\phi _0,\phi _1,\phi _2)=+f(\phi _0+\phi _0\phi _1+\phi _0\phi _1\phi _2).$$
(9)   
This is not the only possible choice, but given the structure of the Hamiltonian (2), this is a natural one. Another possible choice is simply $`F=f(\phi _0+\phi _1+\phi _2)`$. Note that with $`f`$ positive, the drag force acts against the direction of the motion of the motor.

In figure 2 we show the efficiency $`p`$ versus drag $`f`$ for different temperatures $`T`$. We observe that $`p`$ decreases as the drag force is increased. For high temperature the efficiency $`p`$ decreases approximately approximately linearly with $`f`$. At lower temperatures one observes that a very high efficiency is maintained even for moderate drag. At larger drag, the motor stops moving forward. The stalling at $`f=1`$ occurs because the energy-minimum of $`H_0`$, Eq. (1), which is equal to -3, is destroyed by the contribution of the drag term, which is $`3f`$ when $`f=1`$. For $`f>1`$, the state $`(\phi _0,\phi _1,\phi _2)=(0,0,0)`$ has lower energy that the state $`(1,1,1)`$, and the ATP-cycling looses its effect. The net result is that the motor stalls. The question now is, what temperature should we choose in the model to compare with actual motors. The $`ATP`$ cycle is known to generate about $`25kT_{room}`$ and the total binding energy af a protein domain is of the same order. Further motor proteins stall at a drag corresponding to a work per step of about $`10kT_{room}`$. In the model the total binding energy is $`3`$ and the ATP cycle generates $`4`$ units of energy. Thus room temperature corresponds to a temperature in the model of about $`0.2`$. In the discussion above, this is what we mean with low temperature. Thus our model predicts high efficiency maintained nearly up to stalling drag.

Finally we would like to remark that if we pull on the motor, i.e., employ a negative $`f`$, the success rate increases for some range of pulls, until finally the efficiency of the motor drops dramatically. This drop is because for $`f`$ large and negative both values of $`A`$ lead to the same ground state. To be quantitative for the case $`A=4`$: For $`[\text{ATP}]=0`$ the ground state is $`(1,1,1)`$ for all $`f<0`$. For $`[\text{ATP}]=4`$, then for $`f>1/3`$ the ground state is $`(0,0,0)`$ whereas for $`f<1/3`$ the ground state is again $`(1,1,1)`$. Thus for $`f>1/3`$ the motor switch between the ground states $`(0,0,0)`$ and $`(1,1,1)`$ when the ATP variable cycles. However when $`f1/3`$, the $`(1,1,1)`$ state becomes the ground state for both $`[\text{ATP}]`$ values, and the ATP-cycling no longer forces the motor to switch between states. The result is a drop in efficiency. In Figure 2, the drop occurs at a smaller $`f`$ than $`1/3`$, but seems to approach this value as the temperature is decreased.

We now discuss how the present model is different from existing ones. It has previously been proposed that motors could work as ratchets . Our model is indeed a type of ratchet, it cycles between two states, one of random diffusion and one of directed motion, much like the sawtooth ratchet originally proposed by Prost et al. . However a ratchet mechanism similar to the one studied by Prost et al. would, dependent on the asymmetry of the potential, at most make one positive move at half the ATP hydrolysis events. The other half of the ATP cycles, it will remain in same potential well, or maybe even stop. Thus the maximum efficiency would be $`1/2`$. In this letter we instead propose, that forward motion depends on the relative ordering of two events associated to two different degrees of freedom. This results in a motor which is close to 100% efficient.

In summa the present paper discusses how ordering of events may be utilized to construct a simple motor. The motor contains three variables $`\phi _0`$, $`\phi _1`$ and $`\phi _2`$. However, the hierarchical structure of the Hamiltonian (2) is easily extended to any number of variables — and thereby levels. The hierarchical nature of the Hamiltonian ensures that each level controls all subsequent levels, that is we have an explicit realization of local control of global motion as seen in allosteric proteins. Furthermore, the model suggests a connection between two seemingly unrelated properties: folding and motor action.