Subunit organization in the Dam1 kinetochore complex and its ring around microtubules
https://reasonandscience.catsboard.com/t2107-subunit-organization-in-the-dam1-kinetochore-complex-and-its-ring-around-microtubules
One Ring to Bind Them All 2
A Smart, Elegant Solution to Preserving Genetic Integrity
A mystery surrounding tubulin, the protein that plays a crucial role in the passing of genetic material from a parent cell to daughter cells, has been at least partially solved. Fibers of tubulin — or microtubules — interact with the complex of proteins known as the kinetochore and cause the kinetochore to assemble a ring around these fibers.
There is a smart and elegant solution to the problem of controlling microtubule dynamics during mitosis. Mitosis is the process by which a dividing cell duplicates its chromosomes and distributes them equally between its two daughter cells — a process in which mistakes can lead to cancer and birth defects. ( that means, the process had to be functional and fully operational right from the beginning, otherwise, cell division would not be possible ) To ensure the equal distribution of chromosomes, spindles of microtubules attach to a chromosome's centromere through Kinetochores. (The centromere is the central region where the two chromatids that make up a chromosome connect.)
The Dam1 kinetochore complex forms a ring which promotes the stability of microtubules in spindles and allows for the continued attachment of microtubules to the kinetochore. Yet at the time, the dynamics behind the ring formation, critical to understanding and possibly exploiting the process, remained unknown.
When microtubules encounter Dam1 kinetochore complexes, they induce the complexes to undergo a large conformational change, forming kinks that give them the necessary shape to self-assemble themselves into a ring structure.
Question: How did the genetic code come up with that mechanism? trial and error of the genetic sequence until providing the correct assembly instructions ? would the assembly not be possible only AFTER the right genetic instructions were in place? Why is it not far more rational to infer that intelligence programmed the mechanism with the end goal in mind?
When microtubule spindles encounter Dam1 kinetochore complexes, the complexes self-assemble into a ring around the microtubules. This tubulin tail is very acidic and it makes a cloud of negative charges around the microtubules, which the Dam1 ring grabs hold of. This electrostatic means of holding onto the microtubules is not so sticky or tight, but instead allows for lateral sliding of the Dam1 rings along the microtubules."
So that's a finely tuned mechanism through electrostatic forces. Amazing!
There is also a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules. Without this region, the ability of the Dam1 to form a ring is reduced.
That is a pre-programmed very important communication process, which also had to be fully functional right from the start.
The mechanism of closing the subunits resembles human-made bracelet chains: One cannot deny that the ring structure appears strongly with human-made designs, is, however, more complex and has advanced functional goals, and is fine-tuned through electrostatic forces for lateral sliding of the Dam1 rings along the microtubules. This is a beautiful solution to make use of microtubule dynamics which permits clearly to infer intelligent design.
It was once thought that kinetochores contain molecular motors that enable them to propel their attached chromosomes along the microtubule spindles. Now it is known that chromosomal separation occurs even if possible motors are removed from the cell — so as long as the microtubules themselves are allowed to remain dynamic. When microtubule fibers come to the kinetochore, the kinetochore forms a ring around the microtubule it engages, stabilizing it in the process. Later in mitosis, when the microtubules are forced by other proteins to break apart, the peeling of the microtubule wall pushes the ring toward each of the two daughter cells. Thus the ring utilizes the breakdown of microtubules as an energy source. Along with a microtubule spindle, keeping it segregated from other chromosomes during cell division. Segregation is critical for preventing mistakes that can lead to cancer and birth defects.
Dam1 complex dimers are shown in blue and gold ( see below ) , with some complexes in solution and others associated
with the outer region of the kinetochore (black lines). When they encounter a microtubule, the Dam1 complexes
self-assemble into a kinetochore ring (bottom). As the microtubules break down, the ring is pushed outward along
the fibers toward the daughter cells, bringing along the kinetochore and attached chromosome.
The Dam1 kinetochore complex formes a ring which promotes the stability of microtubules in spindles and allows for the continued attachment of microtubules to the kinetochore. Yet at the time, the dynamics behind the ring formation, critical to understanding and possibly exploiting the process, remained unknown.
When microtubules encounter Dam1 kinetochore complexes, they induce the complexes to undergo a large conformational change, forming kinks that give them the necessary shape to self-assemble themselves into a ring structure. ( How did the genetic code come up with the emergence of that mechanism? trial and error of the genetic sequence until providing the correct assembly instructions ? would the assembly not be possible only AFTER the right genetic instructions were in place? ) Why is it not far more rational to infer that intelligence programmed the mechanism with the end goal in mind?
When microtubule spindles encounter Dam1 kinetochore complexes, the complexes self-assemble into a ring around the microtubules.
"This tubulin tail is very acidic and it makes a cloud of negative charges around the microtubules, which the Dam1 ring grabs hold of," says Nogales. "This electrostatic means of holding onto the microtubules is not so sticky or tight, but instead allows for lateral sliding of the Dam1 rings along the microtubules."
So that's a finely tuned mechanism through electrostatic forces. Amazing!
Nogales and her colleagues also identified a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. "These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules," Nogales says. "We have found that without this region, the ability of the Dam1 to form a ring is reduced." So that is a pre-programmed very important communication process, which also had to be fully functional right from the start, otherwise, as the researchers stated, " the ability of the Dam1 to form a ring is reduced. As i remarked here Most signal-relay stations we know about were intelligently designed. Signal without recognition is meaningless. Communication implies a signalling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!” or, in this case, that Dam1 proteins mean “tell the ring when the time is right for it to let go of the microtubules” The transmitter and receiver can be made of non-sentient materials, but the functional purpose of the system always comes from a mind. The mind uses the material substances to perform an algorithm that is not itself a product of the materials or the blind forces acting on them. 3
Any process that is essential to cell mitosis and could easily be blocked is a potential avenue for the treatment of cancer. While the Dam1 kinetochore has so far only been found in yeast, some of its constituent proteins are common to other eukaryote cells. Furthermore, the biophysics behind the Dam1's interactions with microtubules should have analogies in the cells of other organisms, including humans.
"This is such a beautiful solution to make use of microtubule dynamics that it is bound to be repeated elsewhere," Nogales said. "We have found the first ring; surely there are other rings that await discovery."
Dam1-based couplers slide over the microtubule ( MT ) lattice without detaching, and both the growing tip and the coverslip-anchored portion of the MT present barriers to sliding. (a) Selected frames from a movie are shown (Movie 6), beginning with a tip-attached bead under tension (25 s). Reversing the direction of load (i.e., switching to compression) causes the bead to disengage the tip (denoted by the yellow chevron) and slide until it reaches the seed (white arrow), where sliding halts (65 s). Reversing the load again (i.e., reapplying tension) causes the bead to slide back and reengage the tip (75 s). (Scale bar, 5 μm.) (b) Beads located at the growing tip or the anchored seed respond asymmetrically to force: The same magnitude of force that is insufficient to slide them past the barrier, when reversed, immediately causes the bead to slide back away from the barrier. The lower plot shows bead position versus time, and the upper plot shows bead-trap separation after conversion to force by multiplying by the trap stiffness. Gray dots show raw data; black trace shows same data after smoothing with a 500-ms window. Dotted vertical lines mark the time when force was reversed. (c) Ring model for Dam1-based attachment and movement. In this view, between 10 and 16 Dam1 complexes oligomerize into a ring encircling the filament that is large enough to slide over the lattice (arrows) but too small to slide past areas where the filament is widened. Such a ring would be topologically prevented from sliding past the anchored segment of the MT (dotted line at left), as we observed. Growing tips also blocked sliding, perhaps because of the flared protofilament sheets that are thought to occur at assembling tips. Protofilaments (PFs) curl and peel away from the main filament during disassembly and could push continuously against a Dam1 ring to drive movement in the direction of shortening. An alternative model in which coupling is provided by a disordered collection of MT-binding proteins is also consistent with our observations (see Discussion).
The 13-protofilament microtubules are surrounded by 16 repeats of the Dam1 complex oligomerized into a ring, or a turn of a spiral with the most proximal visualized mass of the Dam1 complex positioned ∼20 Å away from the ordered microtubule lattice. This distance and the accommodation of different repeats are achieved via interactions that are mediated by flexible elements in the Dam1 complex (likely in the proteins Duo1p and Dam1p;and the disordered E-hook of tubulin (C-terminal tail of tubulin, highly charged with glutamic acid residues and involved in interaction with a number of microtubule-associated proteins)
the mechanism of closing the subunits resembles human-made bracelet chains: One cannot deny that the ring structure appears strongly with human-made designs, is, however, more complex and has advanced functional goals, and is finely-tuned through electrostatic forces for lateral sliding of the Dam1 rings along the microtubules.
In budding yeast, in which there is a single microtubule attachment per kinetochore, the heterodecameric Dam1 complex has been shown to be an essential component of the yeast outer kinetochore and to form closed rings around microtubules in vitro 2 The ring form of the Dam1 complex is used as a topological constraint to processively “surf” along the depolymerizing end of the microtubule as the protofilaments peel back. The attachment of the Dam1 ring to other kinetochore proteins could then stably tether the chromosome to the end of a spindle microtubule.
1) http://www2.lbl.gov/Science-Articles/Archive/sabl/2007/Oct/onering.html
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216659/
https://reasonandscience.catsboard.com/t2107-subunit-organization-in-the-dam1-kinetochore-complex-and-its-ring-around-microtubules
One Ring to Bind Them All 2
A Smart, Elegant Solution to Preserving Genetic Integrity
A mystery surrounding tubulin, the protein that plays a crucial role in the passing of genetic material from a parent cell to daughter cells, has been at least partially solved. Fibers of tubulin — or microtubules — interact with the complex of proteins known as the kinetochore and cause the kinetochore to assemble a ring around these fibers.
There is a smart and elegant solution to the problem of controlling microtubule dynamics during mitosis. Mitosis is the process by which a dividing cell duplicates its chromosomes and distributes them equally between its two daughter cells — a process in which mistakes can lead to cancer and birth defects. ( that means, the process had to be functional and fully operational right from the beginning, otherwise, cell division would not be possible ) To ensure the equal distribution of chromosomes, spindles of microtubules attach to a chromosome's centromere through Kinetochores. (The centromere is the central region where the two chromatids that make up a chromosome connect.)
The Dam1 kinetochore complex forms a ring which promotes the stability of microtubules in spindles and allows for the continued attachment of microtubules to the kinetochore. Yet at the time, the dynamics behind the ring formation, critical to understanding and possibly exploiting the process, remained unknown.
When microtubules encounter Dam1 kinetochore complexes, they induce the complexes to undergo a large conformational change, forming kinks that give them the necessary shape to self-assemble themselves into a ring structure.
Question: How did the genetic code come up with that mechanism? trial and error of the genetic sequence until providing the correct assembly instructions ? would the assembly not be possible only AFTER the right genetic instructions were in place? Why is it not far more rational to infer that intelligence programmed the mechanism with the end goal in mind?
When microtubule spindles encounter Dam1 kinetochore complexes, the complexes self-assemble into a ring around the microtubules. This tubulin tail is very acidic and it makes a cloud of negative charges around the microtubules, which the Dam1 ring grabs hold of. This electrostatic means of holding onto the microtubules is not so sticky or tight, but instead allows for lateral sliding of the Dam1 rings along the microtubules."
So that's a finely tuned mechanism through electrostatic forces. Amazing!
There is also a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules. Without this region, the ability of the Dam1 to form a ring is reduced.
That is a pre-programmed very important communication process, which also had to be fully functional right from the start.
The mechanism of closing the subunits resembles human-made bracelet chains: One cannot deny that the ring structure appears strongly with human-made designs, is, however, more complex and has advanced functional goals, and is fine-tuned through electrostatic forces for lateral sliding of the Dam1 rings along the microtubules. This is a beautiful solution to make use of microtubule dynamics which permits clearly to infer intelligent design.
It was once thought that kinetochores contain molecular motors that enable them to propel their attached chromosomes along the microtubule spindles. Now it is known that chromosomal separation occurs even if possible motors are removed from the cell — so as long as the microtubules themselves are allowed to remain dynamic. When microtubule fibers come to the kinetochore, the kinetochore forms a ring around the microtubule it engages, stabilizing it in the process. Later in mitosis, when the microtubules are forced by other proteins to break apart, the peeling of the microtubule wall pushes the ring toward each of the two daughter cells. Thus the ring utilizes the breakdown of microtubules as an energy source. Along with a microtubule spindle, keeping it segregated from other chromosomes during cell division. Segregation is critical for preventing mistakes that can lead to cancer and birth defects.
Dam1 complex dimers are shown in blue and gold ( see below ) , with some complexes in solution and others associated
with the outer region of the kinetochore (black lines). When they encounter a microtubule, the Dam1 complexes
self-assemble into a kinetochore ring (bottom). As the microtubules break down, the ring is pushed outward along
the fibers toward the daughter cells, bringing along the kinetochore and attached chromosome.
The Dam1 kinetochore complex formes a ring which promotes the stability of microtubules in spindles and allows for the continued attachment of microtubules to the kinetochore. Yet at the time, the dynamics behind the ring formation, critical to understanding and possibly exploiting the process, remained unknown.
When microtubules encounter Dam1 kinetochore complexes, they induce the complexes to undergo a large conformational change, forming kinks that give them the necessary shape to self-assemble themselves into a ring structure. ( How did the genetic code come up with the emergence of that mechanism? trial and error of the genetic sequence until providing the correct assembly instructions ? would the assembly not be possible only AFTER the right genetic instructions were in place? ) Why is it not far more rational to infer that intelligence programmed the mechanism with the end goal in mind?
When microtubule spindles encounter Dam1 kinetochore complexes, the complexes self-assemble into a ring around the microtubules.
"This tubulin tail is very acidic and it makes a cloud of negative charges around the microtubules, which the Dam1 ring grabs hold of," says Nogales. "This electrostatic means of holding onto the microtubules is not so sticky or tight, but instead allows for lateral sliding of the Dam1 rings along the microtubules."
So that's a finely tuned mechanism through electrostatic forces. Amazing!
Nogales and her colleagues also identified a region in Dam1 essential for the regulation of the complex, by spindle-checkpoint kinase enzymes. "These kinases are signaling proteins that, based on tension in the spindles, tell the ring when the time is right for it to let go of the microtubules," Nogales says. "We have found that without this region, the ability of the Dam1 to form a ring is reduced." So that is a pre-programmed very important communication process, which also had to be fully functional right from the start, otherwise, as the researchers stated, " the ability of the Dam1 to form a ring is reduced. As i remarked here Most signal-relay stations we know about were intelligently designed. Signal without recognition is meaningless. Communication implies a signalling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!” or, in this case, that Dam1 proteins mean “tell the ring when the time is right for it to let go of the microtubules” The transmitter and receiver can be made of non-sentient materials, but the functional purpose of the system always comes from a mind. The mind uses the material substances to perform an algorithm that is not itself a product of the materials or the blind forces acting on them. 3
Any process that is essential to cell mitosis and could easily be blocked is a potential avenue for the treatment of cancer. While the Dam1 kinetochore has so far only been found in yeast, some of its constituent proteins are common to other eukaryote cells. Furthermore, the biophysics behind the Dam1's interactions with microtubules should have analogies in the cells of other organisms, including humans.
"This is such a beautiful solution to make use of microtubule dynamics that it is bound to be repeated elsewhere," Nogales said. "We have found the first ring; surely there are other rings that await discovery."
Dam1-based couplers slide over the microtubule ( MT ) lattice without detaching, and both the growing tip and the coverslip-anchored portion of the MT present barriers to sliding. (a) Selected frames from a movie are shown (Movie 6), beginning with a tip-attached bead under tension (25 s). Reversing the direction of load (i.e., switching to compression) causes the bead to disengage the tip (denoted by the yellow chevron) and slide until it reaches the seed (white arrow), where sliding halts (65 s). Reversing the load again (i.e., reapplying tension) causes the bead to slide back and reengage the tip (75 s). (Scale bar, 5 μm.) (b) Beads located at the growing tip or the anchored seed respond asymmetrically to force: The same magnitude of force that is insufficient to slide them past the barrier, when reversed, immediately causes the bead to slide back away from the barrier. The lower plot shows bead position versus time, and the upper plot shows bead-trap separation after conversion to force by multiplying by the trap stiffness. Gray dots show raw data; black trace shows same data after smoothing with a 500-ms window. Dotted vertical lines mark the time when force was reversed. (c) Ring model for Dam1-based attachment and movement. In this view, between 10 and 16 Dam1 complexes oligomerize into a ring encircling the filament that is large enough to slide over the lattice (arrows) but too small to slide past areas where the filament is widened. Such a ring would be topologically prevented from sliding past the anchored segment of the MT (dotted line at left), as we observed. Growing tips also blocked sliding, perhaps because of the flared protofilament sheets that are thought to occur at assembling tips. Protofilaments (PFs) curl and peel away from the main filament during disassembly and could push continuously against a Dam1 ring to drive movement in the direction of shortening. An alternative model in which coupling is provided by a disordered collection of MT-binding proteins is also consistent with our observations (see Discussion).
The 13-protofilament microtubules are surrounded by 16 repeats of the Dam1 complex oligomerized into a ring, or a turn of a spiral with the most proximal visualized mass of the Dam1 complex positioned ∼20 Å away from the ordered microtubule lattice. This distance and the accommodation of different repeats are achieved via interactions that are mediated by flexible elements in the Dam1 complex (likely in the proteins Duo1p and Dam1p;and the disordered E-hook of tubulin (C-terminal tail of tubulin, highly charged with glutamic acid residues and involved in interaction with a number of microtubule-associated proteins)
the mechanism of closing the subunits resembles human-made bracelet chains: One cannot deny that the ring structure appears strongly with human-made designs, is, however, more complex and has advanced functional goals, and is finely-tuned through electrostatic forces for lateral sliding of the Dam1 rings along the microtubules.
In budding yeast, in which there is a single microtubule attachment per kinetochore, the heterodecameric Dam1 complex has been shown to be an essential component of the yeast outer kinetochore and to form closed rings around microtubules in vitro 2 The ring form of the Dam1 complex is used as a topological constraint to processively “surf” along the depolymerizing end of the microtubule as the protofilaments peel back. The attachment of the Dam1 ring to other kinetochore proteins could then stably tether the chromosome to the end of a spindle microtubule.
1) http://www2.lbl.gov/Science-Articles/Archive/sabl/2007/Oct/onering.html
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216659/
Last edited by Admin on Thu May 14, 2020 9:48 am; edited 5 times in total
