They are tiny, and there are billions of them inside you. Tiny machines, one thousand times thinner than a hair strand but strong enough to carry all kinds of material within your cells. Yes, there is a complex army of tiny machines inside your body performing an amazing array of functions while you sit at home sipping your tea.

Your heart is beating. Its lifelong duty is to pump blood to tissues to deliver essential nutrients. Transportation of nutrients continues from blood vessels to cells and then into subcellular compartments. Inside of a cell, there is a need for sophisticated biomachines which are responsible for transport. Did you know that you were equipped with minuscule motors that transported cargos in your cells? Or about cellular highways where molecular cargos are transported?

There are various proteins called “motors” in the cell. They can convert chemical energy to mechanical energy to produce force and motion in the cellular highways.¹ Amazingly, molecular motors are much superior to man-made motors in terms of energetic efficiency by hydrolyzing ATP to fuel enzymatic reactions. These molecular motors include rotary motors, polymerization motors, nucleic acid motors and cytoskeletal motors.

Rotary motors

Bacterial flagellum, used for swimming, acts as a propeller and uses a rotary motor. It has been suggested that this motor is similar to Fo motor found in FoF1-ATP synthase. FoF1-ATP synthase takes part in the conversion of chemical energy in ATP to proton gradient, or vice versa. This chemical reaction involves mechanical rotation of parts of the complex.

Polymerization and nucleic acid motors

Polymerization motors take role in polymerizations and these polymerizations generate forces for repulsion (Actin or microtubule polymerization), or separation of clathrin buds from plasma membrane (Dynamin).

DNA and RNA synthesis also involves the use of molecular motors such as RNA polymerase (RNA synthesis from DNA), DNA polymerase (DNA synthesis), Helicases (separation of double stranded DNA prior to DNA or RNA synthesis), Topoisomerases (removal of supercoiling of DNA), RSC, SWI/SNF, and SMC proteins (Chromatin remodeling and chromosome condensation). Moreover, there are specific viral DNA packaging motors that pack tightly viral DNA into capsids. separation of double stranded DNA prior to DNA or RNA synthesis), Topoisomerases (removal of supercoiling of DNA), RSC, SWI/SNF, and SMC proteins (Chromatin remodeling and chromosome condensation). Moreover, there are specific viral DNA packaging motors that pack tightly viral DNA into capsids.

Cytoskeletal motors

Dyneins, kinesins and myosins denote the three major classes of molecular motor that moves along cytoskeletal structures. Myosin is among the most prominent of motor proteins that takes role in muscle contraction. Kinesin operates on microtubules (long tubes composed of dimers of the protein tubulin, arranged to form 13 parallel tracks) to move cargos inside the cells away from the nucleus (toward positive end of microtubules) and play essential roles in the formation of spindle apparatus and axonal transport. Dynein is also known to transport cargo but in the opposite direction to Kinesin, towards the cell nucleus (toward minus end of microtubules). In addition, dynein is required to beat cilia and flagella.

How molecular motors move

Myosin and kinesin are structurally similar in terms of being dimeric with two motor heads, two legs, and a common stalk. The head regions control the forward movement by binding itself to actin or microtubule filaments. Movement is facilitated by the consumption of ATP by ATPase sites. It is fascinating how these motors translate chemical energy into motion and still be different to the movement of cars. There are different proposals as to how molecular motors move, such as walking (hand-over-hand model), inchworm model, and biased diffusion model.

The-hand-over-hand model suggests that ATP binding induces a conformational change in the forward head movements and keeps fixed, thus leading to the movement of the rear head forward and vice versa. This model, which is also known as the walking model, is similar to upright walking where one foot moves forward while other stay fixed, and vice versa. On the other hand, the inchworm model suggests that only forward head movements use ATP and leads while the other head follows. Studies on the Myosin VI with shorter legs suggested a biased diffusion model. In the diffusion model, the motor moves randomly to the next binding site in a forward direction. In order to find out which mechanism used by molecular motors, scientists measured how much of the head moves following staining with a fluorescent dye. Since molecular motor movements are so small (5-10 nM), optical traps and cantilever probes (>100 μm) were not useful to watch head movements. By increasing both photostability and brightness of organic dyes, Dr. Yildiz at UC Berkeley was able to measure head movements down to 1.5nM scale.

Kinesin: A molecular motor that walks

Kinesins are among microtubule-based motors recently shown to walk like a mountain climber by swapping its two motor units (analogous to feet) in a hand-over-hand mechanism rather than an inchworm mechanism. This recent discovery sheds light on how kinesin moves its cargos such as membrane components, messenger RNA, signaling moleculers, and others along microtubules. In addition, as suggested by findings of Dr. Yildiz, kinesin demonstrates an asymmetric walking where motor heads alternate with slow and fast steps. Further studies using advanced microscopy techniques (called FIONA) which allow nano scale detection of movement down to 2nM resolution demonstrated delicately that processive kinesin motor takes about 8 nM steps (eight-billionths of a meter) for each ATP molecule consumption with alternating 16-nm and 0-nm steps. Furthermore, kinesin is attached to the microtubule while it waits for ATP between steps. Since kinesin is used for long distance cargo transport on relatively big highways of a cell, it elegantly demonstrates a processive motor that reliably travels in a coordinated manner. Of course, not all motors will be moving like kinesin.

Dynein moves through uncoordinated stepping of ring domains

Another motor protein involved in long distance cargo transport is dynein. Dynein is a staggering giant which is much bigger and complex than kinesin and myosin motors. There are about 15 types of dyneins known to take role in cilia and flagella movement and 2 cytoplasmic forms. Cytoplasmic dynein is a homodimeric AAA+ (ATPases associated with cellular activities) motor that transports toward the microtubule minus end, acting opposite to kinesin. FIONA assay demonstrated that the heads moving processively but independently. This mechanism is quite different from the hand-over-hand stepping of kinesin and myosin, for dynein’s steps are not strictly coordinated and highly variable. Most of the time, dynein heads move alternatively with variable head-to-head distance of about 5-50nM. Each head of dynein mostly does not pass each other.

Elegant design, efficiency in transportation and being part of the living system makes molecular motors in the cells superior to man-made motors. Molecular motors travel on cellular highways in the cellular microcosm in the manner of dutiful officials of a king traveling in his domain in security via the fastest modes of transportation and easily cross provincial boundaries, demonstrating more evidently that the Sovereignty of the Eternal King is limitless. Indeed, the signs of His Dominion are reflected by each and every entity from the microcosmic world to macrocosmic universe.

Note

1 Cellular highways are composed of microtubules, microfilaments and actin filaments. Myosin moves along microfilaments through interaction with actin, but dynein and kinesin move along microtubules through interaction with tubulin

References

• DeWitt MA et al. Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains. Science. 2012 Jan 13;335(6065):221-5. Epub 2011 Dec 8.
• King SM. AAA domains and organization of the dynein motor unit. J Cell Sci. 2000 Jul;113 ( Pt 14):2521-6.
• Wilhelm J. Walter & Stefan Diez. A staggering giant. Nature. Vol 482. 2 February 2012.
• Molecular motors and Motor proteins. Retrieved from Wikipedia on 3/31/2012.
• Yildiz et al. Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization. Science 27 June 2003:Vol. 300 no. 5628 pp. 2061-2065
• Yildiz et al. Kinesin Walks Hand-Over-Hand. Science 30 January 2004: Vol. 303 no. 5658 pp. 676-678

Futile cycles are described as two opposing biological reactions that take place in a cell at the same time [1, 2]. As a result, futile cycles have seemingly zero net gain for the cell. Actually, because no process is 100 percent efficient, some energy is lost as heat. Thus, these cycles may even cost cells some energy. They were named “futile” cycles because scientists thought that it was wasteful for a cell to operate two exactly opposite processes simultaneously.

One such process occurs in the powerhouses of cells, the mitochondria. Mitochondria are the places where a process called “oxidative phosphorylation” takes place. Oxidative phosphorylation is an efficient way of producing ATP, the cellular energy currency [1]. In this process, high-energy electrons in nutrients are used to generate potential energy, which is in turn used to produce ATP.

Scientists who worked on mitochondrial function were flabbergasted to discover a family of proteins in the mitochondria that had a strange function. These proteins were dissipating the potential energy in the mitochondria before it could be used to produce ATP. They were named “uncoupling proteins” because they were uncoupling the potential energy buildup from ATP production [3]. Scientists couldn’t imagine what these wasteful proteins were doing in our mitochondria. Uncoupling proteins were decreasing the ATP production efficiency of mitochondria. Therefore, they named this process a futile cycle, where electrons from food were used for building up a potential, and an opposing action of uncoupling proteins were dissipating this potential before it could be stored as ATP [4]. This was similar to short-circuiting a battery by connecting two poles with a wire, and just discharging the energy—energy is lost but no work is done. The scientists took this process as a remnant of a random evolutionary process that was left unfinished—“futile,” with no function at all.

It took several years and the work of a different team of biologists to figure out the benefit of these uncoupling proteins [5]. The scientists were working on the differences between wasps and honey bees. One striking difference between these species was in their ability to adapt to colder temperatures: honey bees couldn’t fly and collect pollen when the outside temperature dropped below 10 C (50 F). They had to stay in their beehives to keep warm. On the other hand, wasps could fly around in colder temperatures. The researchers discovered that the main difference that accounted for this phenomenon was that honey bees didn’t have uncoupling proteins in their mitochondria, while wasps did. Therefore, it became apparent that the main function of uncoupling proteins was to generate heat for the body to stay warm during the times when outside temperatures fell. The uncoupling proteins, it seemed, were generating heat while dissipating the potential energy (just like the wire that heats up when you connect two poles of a battery in short circuit). Later on, it was discovered that these proteins had crucial functions in all warm-blooded animals, especially in ones that hibernate during winter.

In this case, an event that initially appeared to be meaningless or even stupid turned out to be indispensible for supporting life under certain circumstances. The fact that we cannot see wisdom behind certain events does not mean they are random or meaningless. Perhaps it is just a matter of time when, in some context, the seemingly futile thing will have a vital role. So the question remains: is there really any such thing as “random” or “futile”?

References

1. Alberts, B., J.H. Wilson, and T. Hunt. 2008. “Molecular Biology of the Cell.” 5th ed. New York: Garland Science. xxxiii, 1601, [90]

2. Available from: http://en.wikipedia.org/wiki/Futile_cycle#cite_note-0.

3. Nedergaard, J., D. Ricquier, and L.P. Kozak. 2005. “Uncoupling Proteins: Current Status and Therapeutic Prospects.” EMBO Rep. 6(10), p. 917–21.

4. Jezek, P. and J. Borecky. 1998. “Mitochondrial Uncoupling protein may participate in futile cycling of pyruvate and other monocarboxylates.” Am J Physiol, 1998. 275(2 Pt 1): p. C496–504.

5. Staples, J.F., E.L. Koen, and T.M. Laverty. 2004. “Futile Cycle Enzymes in the Flight Muscles of North American Bumblebees.” J Exp Biol. 207(Pt 5): p. 749–54.