User:Brian P. Josey/Notebook/2009/09/01

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Notes of Papers

 * Larry asked me to look at a paper, "Force production by single kinesin motors" by Schnitzer et. al. He wanted me to find how the authors derive three of the equations, 2,4 and 5.
 * Unfortunately I was unable to resolve this issues for him. I will return to the paper at a later date to see if I can understand it more.

However we did discuss the paper that I read last week, "Mechanical Design of Translocating Motor Proteins" by W. Hwang. The paper is a review of how basic motor proteins move in the cell. The authors suggest that we currently know enough about these proteins to create what is essentially a mechanical parts list that are necessary for the proteins to move. They then go on to explain the basic mechanics of how the proteins propagate. While they discuss a wide variety of different proteins, my notes will be limited to the discussion of kinesin due to its relevance to my own work.

There are a few key characteristics of the proteins that can be measured. They are:
 * Unloaded Velocity- The unloaded velocity is essentially the maximum speed that the protein goes when it does not encounter any obstacles or has a load. This occurs when the load is not present and there are no obstacles in the way of protein. Because there is no load, there is a minimum amount of drag, although there still is some drag from the movement relative to the surrounding medium. For Kinesin-1 the typical unloaded velocity is ~700nm/s.
 * Stall Force- The stall force is how much force is need to stop the motor from moving. For Kinesin-1 this typically falls in to the range of 5-7 pN.
 * Step Size- The step size is simply how far the protein can go in a single step, which for kinesin is 8 nm, a value that correspond to the size of a tubulin dimer.
 * Processivity- Processivity can be thought of as how far the motor can go along its path when unloaded. Kinesin is noted to have a higher processivity compared to other motors. The authors note that a protein that keeps its motor heads out of phase with each other in their steps is prone to have a higher processivity. Also, if proteins work as a group by forming pairs and binding to the same cargo this also increases the processivity. They do not state how this would work, but I figure that it is because one can take over for both if the other disassociates from the track, giving it time to reattach.
 * Efficiency- How efficient the motor is is simply the maximum amount of work that can be done divided by the change in free energy. For kinesin, with a stall force of ~6pN and a step size of 8.2 nm the efficiency is 48-60%

From here the authors continue on with a list of mechanical parts that are necessary for the protein to do its function, namely to move along a track while transporting a cargo.

Force Generator- When the transducer undergoes a conformational change, it links to the force-generator and produces a power stroke. This power stroke causes the protein to move forward a single step, with a successive number of power strokes generating the movement of the protein. The authors note that the link of fuel processor to transducer to force generator is not necessarily mechanical, the free energy associated with the change in the protein can also be used to generate force. Some motor proteins can create a rapid thermal fluctuation in one direction by virtue of their conformational change. In kinesin, there is a slight change in entropy between the forward and backward steps that supports movement in the forward direction.
 * Fuel- Obviously the fuel that powers the protein is an integral part of the mechanism. Without a proper fuel source, the motors will not work. For kinesin it is a well established fact that the hydrolysis of ATP is the fuel source.
 * Transducer- The transducer converts the chemical energy into a mechanical force, resulting in the movement of the motor protein. The chemical use of the fuel alone for movement would not be efficient for it is difficult to direct it without the transducer.
 * Lever- The lever is part of the molecule that actually moves, taking the steps. It should be noted that in kinesin, the lever has some overlap with the force generator.

Together all of these can be combined, creating a model of how kinesin walks:


 * When kinesin starts off stationary on the microtuble, the hydrolysis of an ATP molecule on the aft head forces it to release its grip on the microtubule, by reducing its affinity for attachment.
 * There is a slight conformational change in the neck linker which prevents the aft head from reattaching to the microtubule.
 * The power stroke moves the aft head forward, towards the next step position in the microtubule.
 * The now leading head releases ADP and binds strongly to the microtubule, completing one cycle of the stepping process.


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