Inner World of the Cell

Molecular Motors :

Kinesin, Myosin, Replication Motors, Ribosome, Molecular Pumps

Kinesin - This portein has a size of about 20 nm. As shown in Figure 06, the kinesin has two heads (should be "feet" anatomically) at the bottom linked together by a short neck, which condemns the molecule to waddling. The coiled stalk provides flexibility, while the cargo-binding tail (again should be head in analogy with a "being") carries the load. Hydrolysis (break down by interacting with water, i.e., H₂O + ATP

ADP + p_i^§ + energy) of the ATP in the pocket releases the hind foot from the binding with the microtubule allowing

		it to swing forward 16 nm (Figure 09). The cycle repeats at a rate of about 7 steps per second. It can move as fast as 500 nm/sce by raising the ATP concentration. While the kinesin moves along the microtubule toward the "-" end at the MTOC (Figure 05) the dynein proceeds in the opposite direction. Dynein is a variation of kinesin, which belongs to families of more than one hundred kinds of slightly different forms on a common theme.
Figure 09 Kinesin [view large image]	Figure 09a Kinesin Video	^§p_i = H₂PO₄^2- (inorganic phosphate) The 35 mins YouTube video presents a lot more details.

[2023 Update]

The selected molecule is tagged with fluorophore, which is any molecule with the ability to absorb light and emit it at some other well defined wavelength. A donut-shaped laster beam (with zero intensity at the center, see the "M" shaped curve in Figure 09b,a).

The position of the molecule (together with the fluorophore) is attained when the number of re-emitted photons is at the minimum. This is very close to the coordinates of the center of the donut-shaped laster beam (see Figure 09b,b).

Figure 09b,c illustrates the process with the laser beam getting closer and smaller in the attempt to cover the fluorophore, i.e. the molecule.

Figure 09b
MINFLUX View

Figure 09b,d shows the trajectory of the molecule by following its motion with the laser beam in time resolution in micro-second range.

There are 2 papers published on March 10, 2023 about this subject :
"MINFLUX dissects the unimpeded walking of kinesin-1" to introduce the MINFLUX microscope that can record protein movements with up to 1.7 nanometer per millisecond spatiotemporal precision.
and "Direct observation of motor protein stepping in living cells using MINFLUX" to apply the MINFLUX microscope in live-cell tracking of single fluorophores with nanometer spatial and millisecond temporal resolution.

These researches confirm what has been known since 1985 (see "Kinesin") but more precise. The kinesin is the end product of 3.6 billion years of evolution of life starting from a bag of un-related molecules (see "Structure in a Cell" and pre-life image

)

[End of 2023 Update]

Myosin - Myosins comprise a family of ATP-dependent motor proteins. They are best known for their role in muscle contraction and in a wide range of other eukaryotic motility processes. Similar to the kinesins, most myosin molecules are composed of a head, neck, stalk, and tail domain except for the longer neck so that they can "walk" toward the "+" end (at the cell membrane) along the actin. Figure 10 show s the sequence of cargo delivery by the myosin from free floating to the final ditching of the cargo at the cell surface. Figure 11 illustrates a slightly different scenario by fetching the cargo from the kinesin :

(A) Free floating, (B) Attachment to the cargo carried by the kinesin, (C) Transferring from the microtubule track to the actin track (Arp2/3 is the site for the formation of actin) swing forward 16 nm (Figure 09). The cycle repeats at a rate of about 7 steps per second. It can move as fast as 500 nm/sce by raising the ATP concentration. While the kinesin moves along the microtubule toward the "-" end at the MTOC (Figure 05) the dynein proceeds in the opposite direction. Dynein is a variation of kinesin, which belongs to families of more than one hundred kinds of slightly different forms on a common theme.

Figure 10 Myosin
[view large image]

Replication Motors :

		1. Topoisomerase - It is the leading motor in the process. Its job is to untwist the helix, which would be twisted around as the two DNA strands become unwound (see insert in Figure 12). This pacman-like enzyme makes an incision that breaks the DNA backbone, so they can then pass the DNA strands through one another, swivelling and relaxing the DNA before re-sealing the breaks.
Figure 11 Cargo Haulling	Figure 12 Topoisomerase, Helicase and Polymerase [view large image]	The name is derived from the action in breaking (-ase) the DNA into an isomer with different topological form.

2. Helicase - Structurally, helicase looks like a six-lobed rotor with a hole in the middle through which DNA passes. It splits the two strands by lowering the binding strength. The mechanism for the motion along the track, i.e., the DNA is not clear. Since the polymerase can run only in the 5' to 3' direction (for the new strand), the replication is more complicated for the lagging strand. Short DNA (by the name of Okazaki fragments) have to be linked together as the polymerase keeps moving back to produce them. The DnaG (associated with the helicase, see Figure 12) synthesizes an RNA primer every few kilobases (kb). These primers prevent the synthesis of the Okazaki fragments by the DNA ligase (not shown) until its removal (also see DNA).

3. Polymerase - DNA polymerases have highly conserved structure, which means that their overall catalytic subunits vary very little from species to species and implies its indispensable nature in life. It is composed by a combination of three lumps. One domain appears to function in catalyzing the transfer of phosphoryl groups in the phosphoryl transfer reaction. Another domain functions to bind the nucleotide triphosphate to the deoxyribose in creating the template base. The third plays a potential role in the processivity (nucleotides counting), translocation (segment transfer) and positioning of the DNA.

Ribosome - Ribosome is the site for protein synthesis by reading information from the mRNA track. It consists of two

	subunits, a large and a small one. As shown in Figure 13, each unit includes one of two strands of rRNA (ribosomal RNA) and some protein subunits as its components. The unit "S" in the diagram is called "svedberg", which is the rate of sedimentation. It is sufficient to know that high number of svedberg corresponds to bigger molecule. See more detail about translation to protein in RNA.
Figure 13 Ribosome

Molecular Pumps - Some molecular machines do not rely on track to function. Most of them are various ion pumps sitting on the cell membrane. Many of the pores on the membrane are passive allowing the material to diffuse along the gradient. But there is a

		requirement to re-establish the gradient, otherwise nothing would move in or out once the equilibrium is reached. Such needs are fulfilled by the active pores or pumps, which restore the non-equilibrium environment at the expense of some energy. Figure 14 and 15 are examples of ion pumps - the sodium pump is used in producing the action potential, while the proton pump is for the synthesis of the ATP's. It is the concentration gradient of the ions that they are used to restore (see more detail in Bio-electricity).
Figure 14 Sodium Pump [view large image]	Figure 15 Proton Pump [view large image]