Biomolecular machines

[rwenzori]

Intelligent typesetters? Mmmm. Even bacteria have those.

How I wish these biologist types would stop anthropomorphising.

 

[Phronesis]

How Mitochondria Get Their Membranes Bent

ScienceDaily (June 24, 2009) — Mitochondria are the powerhouses of cells. Underneath their smooth surface they harbor an elaborately folded inner membrane. It holds a multitude of bottleneck like invaginations, which expand into elongated cavities (cristae). The narrow shape of the entrance or pore to the cristae ('crista junction') allows separation of the intracristal space and storage of molecules. Cytochrome c, for example, an important signaling protein in programmed cell death (apoptosis), is stored in this compartment.

When apoptosis is triggered, the pores enlarge and cytochrome c is released into the cytosol. Thus, understanding of how the pore diameter and the shape of the inner membrane are regulated on a molecular basis is of great relevance to a better understanding of mitochondrial function in general. Recently, in cooperation with other research teams, the group of Prof. Andreas Reichert, who has been appointed as professor for Mitochondrial Biology to the Goethe University within the Cluster of Excellence Macromolecular Complexes in 2007, has identified two proteins linked in an antagonistic manner that are relevant for governing inner membrane structure.

In the current issue of the the Journal of Cell Biology Rabl, Soubannier et al. report on their quest of slow-growing baker`s yeast mutants harboring deformed mitochondria. Thereby, they discovered the protein Fcj1 ("Formation of criasta junction protein 1"), which is embedded in the inner membrane and accumulates at crista junctions. Upon increased expression of Fcj1 the number of cristae junctions goes up. Without the protein, however, crista junctions are lacking and the inner cristae membrane forms internal parallel stacks of vesicles.

On the other hand, the researchers found that regular assemblies (supercomplexes) of the F1FO-ATPase, a protein complex required for supplying the cell's energy, accumulated at the cristae tips but were less abundant at crista junctions. In addition, Fcj1 and the F1FO-ATPase appear to have opposing functions. In fact, Fcj1 reduces the formation of F1FO-supercomplexes. "We hypothesize, Fcj1 makes sure that the membrane can adopt a negative curvature, while the F1FO-ATPase supercomplex induces positive bending", Andreas Reichert interprets the results. "This is highly exciting, as we have for the first time found out how mitochondrial ultrastructure is regulated and which components determine the structure of crista junctions at all."

 

[Phronesis]

A little more information about nuclear pores:
Video and a few images:

And a few recent discoveries:
First Detailed Map Of Nuclear Pore Complex Made
New Model Of A Nuclear Pore Complex Is Based On Crystal Structure Of Its Key Component
3-D Structure Of Key Nuclear Pore Building Block Identified

In new research, scientists have for the first time glimpsed in three dimensions an entire subcomplex of the NPC; it's the key building block of this little understood and evolutionarily ancient structure, an innovation fundamental to the development of nearly all multicellular life on earth.

The findings, by Martin Kampmann, a graduate student in John D. Rockefeller Jr. Professor Günter Blobel's Laboratory of Cell Biology, add details to an unfolding picture of cellular evolution that shows a common architecture for the NPC and the vehicles that transport material between different parts of the cell, called coated vesicles. As early as 1980, Blobel proposed that internal membranes of cells – such as those encompassing the nucleus and vesicles – evolved from folds or invaginations of the outer cell membrane.

Rockefeller scientists Brian Chait and Michael Rout suggested in a 2004 paper in PLoS Biology that both the NPC and vesicle coats, which contain similar protein folds, evolved from ancient membrane-coating proteins that stabilized these primordial internal membranes. "So far, it's been unclear how these ancient folds work in the nuclear pore complex", Kampmann says. "Now we can see that the α-solenoid folds form long, flexible arms and hinges that end in the more compact, globular β-propellers. The same architectural principle is found in clathrin, a common component of vesicle coats."

In research to be published online June 7 in Nature Structural & Molecular Biology, Kampmann isolated and purified samples of the most fundamental building block of the NPC known as the Nup84 complex, which is composed of seven proteins. The entire NPC – enormous by molecular standards – consists of 30 different kinds of proteins. Focusing on the Nup84 complex, Kampmann used an electron microscope (EM) to take thousands of images of the complex in different states or conformations, which could reflect a role in the expansion and contraction thought to facilitate the passage of various sized molecules through the NPC. By computationally averaging these many different views, he reconstructed the first three-dimensional models of the Nup84 complex. Finally, based on prior work in the Blobel lab using X-ray crystallography to determine the exact atomic structure of individual proteins in the Nup84 complex, he plugged these proteins snugly into the EM structure.

"Because the nuclear pore complex is probably too big and flexible to determine its entire atomic structure by X-ray crystallography, I think this three-dimensional EM approach could be a big help in solving the whole thing," Kampmann says. "It allows us to put the crystal structures that we do have in context." Kampmann is applying the EM approach to other subunits in hopes of fleshing out the overall picture of one of the most mysterious machines in molecular biology. "Martin's data represent an important advance toward piecing together the structure of the NPC," Blobel says.

Given the central role of the nuclear pore complex in the most basic cell processes, defects in its assembly, structure and function can have lethal consequences. Its proteins have been associated with viral infection, primary biliary cirrhosis and cancer. An understanding of how the complex works could lead to treatments for these diseases, and also reveal the evolutionary coup that led to the gene-protecting structure found in every cell more complicated than the simplest single-celled microorganisms: the nucleus.

 

[Phronesis]

More irritating science for the non-teleological, non-intentional, truth-questioning zombies .

Structural Biology Scores With Protein Snapshot

ScienceDaily (June 25, 2009) — In a landmark technical achievement, investigators in the Vanderbilt Center for Structural Biology have used nuclear magnetic resonance (NMR) methods to determine the structure of the largest membrane-spanning protein to date.

Surface-filled representation of diacylglycerol kinase. The "porch-like" structure of the enzyme is highlighted, and the substrate diacylglycerol is depicted bound to the active site. Investigators at the Vanderbilt Center for Structural Biology used NMR methods to determine the structure of diacylglycerol kinase, the largest membrane-spanning protein studied by NMR to date. (Credit: Charles Sanders, Ph.D., Vanderbilt University Center for Structural Biology)​

Cells Use Import Machinery To Export Their Goods As Well​

ScienceDaily (June 25, 2009) — In the bustling economy of the cell, little bubbles called vesicles serve as container ships, ferrying cargo to and from the port - the cell membrane. Some of these vesicles, called post-Golgi vesicles, export cargo made by the cell's protein factory. Scientists have long believed that other, similar vesicles handle the reverse function, importing life-supporting nutrients and proteins through an independent process.

By using a finely honed type of microscopy to more precisely examine these transactions, new research shows the processes are not as independent as assumed: certain molecules handle cargo moving in both directions. Like stevedores, they're involved in both loading and unloading the cell's container ships.

Jyoti Jaiswal, a research assistant professor and Sanford Simon, head of the Laboratory of Cellular Biophysics at Rockefeller University, examined the most common form of cellular export process called constitutive exocytosis, a continual ferrying of goods involved in the regular life and maintenance of all eukaryotic cells. This sort of shipping was assumed to end with the vesicles fusing completely to the membrane and delivering their whole load of proteins and lipids, in contrast to the more discriminating process by which similar container ships import proteins from outside the cell, called endocytosis. But, in a paper to be published June 26 in Cell, Jaiswal and Simon show that some of the key molecules regulating endocytosis, such as clathrin, dynamin and actin, are also at work in exocytosis.

"In retrospect, it makes perfect sense," Jaiswal says. "But at first we thought we had to be wrong because they had been defined as endocytic molecules." Adds Simon: "Once we took a step back from the dogma, we saw that cells employ these molecules for import and export. Then everything fell into place. We should stop stereotyping molecules as dedicated for this or that purpose. It puts on the blinders. There's an advantage in biology of sometimes just looking without a hypothesis."

The researchers used a special form of microscopy (total internal reflection fluorescence microscopy) capable of focusing solely on the narrow plane in which the vesicle and membrane merge. "It's a little like the guy looking under the streetlight for his keys because it's the only place he can see, but we've actually arranged for the streetlight to be focused on exactly where we're interested," Simon says. "We get the vesicles at the point of fusion without the background noise of everything else going on inside the cell."

For the first time, Jaiswal was able to observe individual post-Golgi vesicles as they deliver cargo in their lumen and cargo carried in the membrane shell that surrounds the vesicle. This ability revealed behaviors that were not expected. The researchers showed first that the most common delivery of post-Golgi cargo is a so-called kiss-and-run exchange in which the vesicle partially merges with the membrane and delivers some, but not all, of its contents. Some vesicles, those packing neurotransmitters, for instance, are mobilized by a flood of calcium to spill their haul, signaling nearby cells.

By adjusting the levels of calcium inside the cell, the researchers definitively found that calcium did not affect constitutive exocytosis of post-Golgi vesicles. Then they successively inhibited three molecules known for their membrane-bending role in endocytosis -- clathrin, dynamin and actin. In the absence of any one of these molecules, the researchers found that the vesicles merged fully with the membrane and disgorged all their cargo, which they had shown was an aberration in exocytosis, not the rule, as had been previously assumed. Together, the experiments demonstrate that cells employ some of the same molecules for importing and exporting cargo. "They use the same machinery for both," Jaiswal says. "This blurs the line between endocytosis and exocytosis. Perhaps we should just call it membrane trafficking."

The researchers do not yet know the function of this regulation of exocytosis. They are investigating other molecules' roles in the process to further understand the role and regulation of this process.

 

[rwenzori]

More irritating science for the non-teleological, non-intentional, truth-questioning zombies .

Is it your intention to try to irritate others?

 

[Phronesis]

No it is just apparent that how interesting discoveries regarding biomolecular machines, you know those functional objects that allow us to reason, irritates people that have a certain non-teleological, non-intentional, truth-questioning, zombie-like outlook on life.

Apologies to these critters, but if this kind of science irritates you (no fault of my own btw), rather not pretend science is going to support whatever outlook you have on life...

 

[Phronesis]

Intestinal Cells Surprisingly Active In Pursuit Of Nutrition And Defense

ScienceDaily (July 6, 2009) — Every cell lining the small intestine bristles with thousands of tightly packed microvilli that project into the gut lumen, forming a brush border that absorbs nutrients and protects the body from intestinal bacteria.

In the June 29, 2009 issue of the Journal of Cell Biology, Matthew McConnell, Matthew Tyska, and colleagues now find that microvilli extend their functional reach even further using a molecular motor to send vesicles packed with gut enzymes out into the lumen to get a head start on breaking down their substrates.

Microvilli have traditionally been viewed as passive scaffolds that increase the surface area of the gut wall. The apical plasma membrane tightly wraps around each protrusive bundle of actin, providing more space for nutrient processing and absorption. The motor protein myosin-1a (myo1a) maintains this structure by connecting the plasma membrane to the actin filaments.

In 2007, Tyska and colleagues found that myo1a functions in isolated brush borders to actively move membrane along the length of the microvilli, like a "membrane escalator." To their surprise, at the top of these escalators—the tips of the microvilli—the membrane pinched off to form small vesicles that were released into the surrounding medium. According to Tyska, when they showed their data to gastroenterologists, they immediately asked "Why would brush borders do that? They're wasting perfectly good apical membrane!" Tyska therefore wanted to see if vesicle shedding was a bona fide physiological function for microvilli.

Sure enough, scanning electron micrographs of rat intestines showed protrusions at the tips of microvilli that looked similar to budding vesicles. And a look at the gut's contents revealed vesicles enriched in the brush border enzyme intestinal alkaline phosphatase (IAP). The vesicles were packed with classical brush border membrane proteins such as aminopeptidases and sugar-processing enzymes, suggesting that the vesicles were derived from microvilli. The vesicles also contained several proteins such as annexin A13 that bend cell membranes and could form part of the vesicle budding machinery.

One protein definitely involved in vesicle formation is myo1a. Myo1a knockout mice still produce lumenal vesicles but they are irregularly sized and no longer enriched in specific proteins like IAP. Tyska thinks that these knockout vesicles are actually chunks of microvillar membrane that are nonspecifically shed when myo1a isn't present to keep them attached to the actin core.

Returning to the gastroenterologists' question: Why would brush borders do that? McConnell et al. showed that the packaged enzymes were exposed on the vesicles' outer surface and were catalytically active. Releasing the enzymes in vesicles might increase their mixing with substrates in the gut's contents. Tyska is particularly interested in IAP, which has recently been shown to detoxify the bacterial outer-membrane component lipopolysaccharide. Releasing IAP in lumenal vesicles could be an important defense mechanism against intestinal pathogens.

Pic of microvilli:

 

[Phronesis]

Molecular Machinery Related To Stem Cell Fate Uncovered

ScienceDaily (July 8, 2009) — The Stowers Institute's Xie Lab has revealed how the BAM protein affects germline stem cell differentiation and how it is involved in regulating the quality of stem cells through intercellular competition. The work was recently published by PNAS Early Edition.

Maintaining the proper balance between stem cell self-renewal and differentiation is critical for normal homeostasis. An imbalance between the two can lead to tissue degeneration and to the development of tumors. It has long been known that the BAM protein is necessary for germline stem cell differentiation, but the specific molecular mechanism underlying BAM function had remained a mystery until now.

Examining the fruit fly ovary, the Xie Lab established that BAM controls stem cell differentiation and competition by interfering with the function of the protein translation initiation factor eIF4A. EIF4A and BAM antagonize each other to regulate the balance between self-renewal and differentiation by promoting proper expression of E-cadherin — a molecule crucial to the stem cell's ability to attach to its microenvironment (its niche).

"Our studies contribute to the understanding of stem cell fate control," said Run Shen, Ph.D., Postdoctoral Research Associate in the Xie Lab and lead author on the paper. "Many protein translation initiation factors have been reported to be unregulated in different human cancer tissues, so our study may help to understand how translational initiation factors participate in stem cell misregulation and the development of tumors."

"Our studies have established the role of BAM as a protein translational repressor using biochemical and genetic tests," said Ting Xie, Ph.D., Investigator and senior author on the paper. "Translational control is very important in regulating gene expression. Many genes critical for stem cell development in the fruit fly germline are suggested to be translational regulators, but their exact roles have not been carefully studied. The knowledge generated by this work and the tests we have developed give us great advantage in tackling many additional questions."

 

[rwenzori]

I see you ( or one of your fellow sockpuppets ) have been pimping your quotemines over at SA Skeptics, though I don't quite see how they are appropriate to that forum. You got sweetly put in your place too, when you began your rudeness LOL!

 

[Phronesis]

I see you ( or one of your fellow sockpuppets ) have been pimping your quotemines over at SA Skeptics, though I don't quite see how they are appropriate to that forum. You got sweetly put in your place too, when you began your rudeness LOL!

Haven't you lied enough about me? Have you got no shame?

 

[Claymore]

Haven't you lied enough about me? Have you got no shame?

Classic troll mock indignation.

 

[Phronesis]

Are you ignorant of the lies about me that this person spreads?

 

[rwenzori]

Haven't you lied enough about me? Have you got no shame?

And how is that a lie? See:

http://forum.skeptic.za.org/science-and-technology/genetic-toolkits-and-multicellularity/
http://forum.skeptic.za.org/science-and-technology/biomolecular-machines/
http://forum.skeptic.za.org/science-and-technology/preadaptations/
http://forum.skeptic.za.org/science-and-technology/quantum-mechanics-and-consciousness/
http://forum.skeptic.za.org/science-and-technology/the-optimality-of-the-genetic-code/
http://forum.skeptic.za.org/science-and-technology/machines-that-make-machines/
etc... etc.

It's just like deja vu all over again LOL!


EDIT: It seems your "machinations" are taking a bit of a pounding over at that forum LOL! Arguments from ignorance, they seem to be. ROFL!

 

[Phronesis]

And how is that a lie?

You said :

I see you ( or one of your fellow sockpuppets ) have been pimping your quotemines

My fellow sock puppets? Sorry, you are a liar.
I have never heard this fellow (teleological)

say that he agrees with this guy (phronesis)

in order to make this guy (Techne) look good

.
neither has fellow (mechanist.)

said or done anything remotely wrong that you can accuse him of sock-puppetry.

Any fool can see those posts are from one author (just different username) unless they are being plagiarized. They are not as I have shown you over and over, and yet you still persist in spreading lies about me all because you seem to think you can score points in a discussion if you fling a little mud (by lying) to the other side. Seen it before... that is all you are good at... flinging poo.
If guess the next thing that you are going to do is moan that I have different usernames? Who cares, like I said, any dumb fool can see I am the author of the posts. (BTW, just in case you don't get it, those pictures are sock puppets, a parody on your lies mmmkay.)

EDIT: It seems your "machinations" are taking a bit of a pounding over at that forum LOL! Arguments from ignorance, they seem to be. ROFL!

It is? Where are the arguments from ignorance? Oh wait... you are lying again to try and score a cheap point for your pointless goal.... Pfff, figures .

 

[rwenzori]

My fellow sock puppets? Sorry, you are a liar.

Oh! I thought I was a lying pig!?!

yet you still persist in spreading lies about me all because you seem to think you can score points in a discussion if you fling a little mud (by lying) to the other side. Seen it before... that is all you are good at... flinging poo.

I don't think so. You appear to be part of a group of sockpuppets, presumably one of whom creates your long essays and quotemines - the one that can actually write English pretty well, and who occasionally debates intelligently. You yourself, from your posts on THIS forum, have a meagre command of English ( as evidenced by your frequent spelling errors, Afrikaansismes, and, of course, by your dog's breakfast of a sig ). You also appear unable to actually debate the long essays you post, resorting rapidly and invariably to endlessly repeated weak insults and denials, demonstrating an unwillingness or a complete inability to comprehend a viewpoint other than your own.

You also habitually tell lies, some of which are really funny, like your claim to have sufficient training and access to facilities and equipment to conduct experiments relating to quantum physics and consciousness. Lollers!

It is? Where are the arguments from ignorance? Oh wait... you are lying again to try and score a cheap point for your pointless goal.... Pfff, figures .

I rather like Anacoluthon64:

Are you being serious!? Having read those linked-to papers (and not just their abstracts, either), it’s clear that none of them actually establishes anything vaguely near what you are claiming. In fact, one is a non-trivial critique of an earlier one. They have no direct relevance to any QM model of consciousness – at very best, merely a peripheral one. Where is this “QM model of consciousness” (my emphasis), please? For that matter, where is any model of consciousness? Because so far, all we’ve been provided with is lots of loose conjecture and irrelevant obfuscation.

Assuming that you are not in fact trying to pull a fast one, it is then obvious that:—

* you haven’t understood a word of what I wrote (or perhaps you simply chose to ignore it);
* you are remarkably innocent on how science proceeds, and
* you know very little of any substance about QM.


You’ll have to do quite a lot better than that. Or are you trying to provide some kind of obscure amusement with these impostures?

'Luthon64

I suppose you have value as entertainment, at least.

Luvvies and huggles.

 

[Phronesis]

Oh! I thought I was a lying pig!?!



I don't think so. You appear to be part of a group of sockpuppets, presumably one of whom creates your long essays and quotemines - the one that can actually write English pretty well, and who occasionally debates intelligently. You yourself, from your posts on THIS forum, have a meagre command of English ( as evidenced by your frequent spelling errors, Afrikaansismes, and, of course, by your dog's breakfast of a sig ). You also appear unable to actually debate the long essays you post, resorting rapidly and invariably to endlessly repeated weak insults and denials, demonstrating an unwillingness or a complete inability to comprehend a viewpoint other than your own.

And your lies continue. What more do you want to show that all those are one and the same PERSON. ME!. knock that into you lying skull.

You also habitually tell lies, some of which are really funny, like your claim to have sufficient training and access to facilities and equipment to conduct experiments relating to quantum physics and consciousness. Lollers!

Uhm, don't hide your lies again. Quote the full conversation please. You said:

I have some understanding of the theory that your first post attempts ( turgidly, as ever ) to articulate. I have not the facilities, the equipment, the specialised training, nor the interest to either verify or falsify it. Nor do you, apart from possibly the interest. It is a controversial theory, interesting, but somewhat speculative. I know you'd love to have Bebeh Jebus weaving patterns in space-time, thereby influencing and monitoring our actions and thoughts, but that is kite-flying, and, besides, it might be that famous Aztec god Pretzlpakit.

Right there you said... I don't have:
1) the facilities
2) the equipment
3) the specialised training

Facilities and equipment?
Let's see.
Access to a multi-core grid? Check.
Access to laboratories and wet-bench skills to do cellular work? Check.
Necessary training to setup and run protein modeling calculations? Check.

Granted the maths and physics are not yet up to scratch to accurately model millions of tubulin subunits in a cellular milleu. Is it part of my project or current studies? No. I just find it interesting and who knows, maybe future studies will focus more on modeling the ORCH-OR hypothesis.

So... you lied again you sad little person. Why don't you post something relevant for a change? Oh wait... non-teleological, non-intentional, truth-questioning, zombie-like critters are not really fond of biomolecular machines. That much is evident from this thread.

 

[rwenzori]

And your lies continue. What more do you want to show that all those are one and the same PERSON. ME!. knock that into you lying skull.

Nay master! To paraphrase Robert Zimmerman, "It ain't you babe". LOL!

Uhm, don't hide your lies again. Quote the full conversation please. You said:

Right there you said... I don't have:
1) the facilities
2) the equipment
3) the specialised training

To study particle decay, and all the other stuff in your spurious QM-consciousness "model"? Who is lying now?

Where are these "facilities" of yours anyway? Or do you make nukes in your garden shed too? Pony up, or shut up, as the saying goes.

So... you lied again you sad little person.

Actually I am neither sad nor little LOL!

You might fool some here, but you don't fool me.

Luvvies and all that.

 

[Phronesis]

Nay master! To paraphrase Robert Zimmerman, "It ain't you babe". LOL!

You just don't get it do you...? You must be in denial.
Here you go again:
Look... at this (check date and compare to this)...and this... and this....oh and this....curious isn't it?
Click, and read with comprehension!

To study particle decay, and all the other stuff in your spurious QM-consciousness "model"? Who is lying now?

Who said you need to study particle decay? ROFL...
Now you can go on and on and try and figure out what I don't have and I have access to. Obviously I don't have access to ALL the necessary equipment to do so. Show me an institution that does btw. However, collaboration is what is needed in this world, and that is something I sure won't get from you ROFL.

You might fool some here, but you don't fool me.

You fool yourself in thinking that you actually post anything constructive ever.

So how about it bubba... gonna post something that is relevant to the thread.... or are you going to continue to show what an aversion atheists and/or non-teleological, non-intentional, truth-questioning, zombie-like critters have for..... biomolecular machines.

 

[rwenzori]

You just don't get it do you...? You must be in denial.

Looking in a mirror again are you?

So how about it bubba... gonna post something that is relevant to the thread....

Yo, bubba, pointing out your BS is relevant, I reckon. Looks like I am in good company - "'Luthon64" just trashed more of your BS over in the Skeptics forum LOL!

 

[Phronesis]

Looking in a mirror again are you?

Oh dear... here it is for you again...
Look... at this (check date and compare to this)...and this... and this....oh and this....curious isn't it?
Click, and read with comprehension!

Yo, bubba, pointing out your BS is relevant, I reckon. Looks like I am in good company - "'Luthon64" just trashed more of your BS over in the Skeptics forum LOL!

Oh, so it is personal for you? Ag shame... must be hard though when you can't even point out your own BS and the only thing you are good at is trash-talking.