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  1. #46
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    The Nature of Cellular Tech 11/30/2006
    For molecule-size entities working in the dark, cellular machines seem pretty clever. Here are some tricks they perform day and night to keep life functioning, described this month in Nature and PNAS. Cell biology is sounding more and more like a mixture of Popular Mechanics and Wired.

    1. Energy balancing act: Cells have to use oxygen without being burned by it. In Nature 11/09,1 Toren Finkel described the delicate way mitochondria deal with their explosive fuel without polluting their environment.

    “Much like any factory producing widgets, mitochondria consume carbon-based fuels. Their product is ATP, the energy currency of the cell. Nonetheless, just like factory smokestacks, mitochondria also release potentially harmful by-products into their environment. For mitochondria, these toxins come in the form of reactive oxygen species (ROS) that include superoxide and hydrogen peroxide. In turn, these oxidants can interact with other radical species or with transition metals to produce by-products that are even more damaging. To combat ROS production, the cell has evolved a number of sophisticated antioxidant defences, including enzymes such as superoxide dismutase to scavenge superoxide, as well as catalase and glutathione peroxidase to degrade hydrogen peroxide.”

    Finkel did not explain how these sophisticated mechanisms might have evolved, except to assert that mitochondria are “tiny and evolutionarily ancient energy-producing organelles.” He did consider a claim that they contain a “design flaw” because they leak measurable amounts of reactive oxygen species. Is this a bug or a feature?

    “If ROS synthesis is so bad, and a molecular solution so apparently straightforward, why has this 'design flaw' not been eradicated during the billions of years of evolution? There are many possible answers, but one is that the notion that ROS from the mitochondria are solely harmful could be incorrect. Indeed, substantial evidence exists that ROS generated in the cytoplasm could have vital signalling functions, and this might also be true for oxidants derived from mitochondria.”

    On closer inspection, then, it appears that “a homeostatic loop exists between mitochondria and ROS and that this loop is, at least in part, orchestrated by PGC-1alpha.” This, in turn, stimulates the production of more oxidant-sweeping molecular machines.

    2. Codes within codes: Helen Pearson wrote a thought-provoking article in Nature 11/16 entitled “Genetic information; Codes and enigmas.”2 The idea is that there is “more than one way to read a stretch of DNA.” Biologists have been searching for hidden meanings in the repetitive and non-coding regions and are turning up codes within the genetic code that affect regulation and expression of genes. The way that DNA is packaged around nucleosomes appears an integral part of the message system. As to how these codes allegedly evolved, she simply asserted that it did, and personified evolution as a designing hand:

    “This elegance is surely the handiwork of evolution – and if the way in which that hand had worked to solve these problems were clearer, the simultaneous decoding of all the messages involved might become easier. Perhaps ancestral organisms had simpler sequence patterns that evolution has optimized, taking advantage of its degeneracy to layer in additional information that helped organisms acquire extra complexity. Hanspeter Herzel, who specializes in statistical analyses of DNA at Humboldt University, Berlin, speculates that the space constraints of the cell may have favoured the development of nucleosomes that wound up unruly DNA – and that their existence then encouraged the evolution of a nucleosome code in the sequence because this lowered the energetic cost of coiling up DNA. But as yet such ideas, and any help they might offer, remain tentative. “We don’t really have a phylogeny of these signals,” he says.”

    Next, Pearson considered that some of the stretches of apparently meaningless code have no biological function at all: they are just there. This approach, though, she finds distasteful: “But to some people the thought of order with no meaning is an affront. To such minds, the idea of teasing out nature’s secrets with little more than mathematical cunning and processing power will never lose its allure.” Stay tuned.

    3. Enzyme ballet: Proteins and enzymes often work in complexes. How do the parts dance without stepping on each other’s toes? How do they get together on a crowded, active dance floor? Two biologists considered this problem in the same 11/16 issue of Nature.3 Pick your favorite analogy; choreography or electrical engineering:

    “Living cells, particularly during growth and proliferation, need regulatory processes of great sensitivity and high specificity. To achieve this, signal-to-noise ratios must be high when information is received and transmitted between the cell surface, the cytoplasm and the nucleus. Just like electrical and engineering control systems, living cells have complex signalling pathways that are moderated by feedback mechanisms. It is becoming increasingly clear that most switches, transducers and adaptors in living systems are created by the assembly and disassembly of multi-component complexes of proteins, nucleic acids and other molecules....
    How do the molecular assemblies in cells achieve the required sensitivity and specificity? Efficient signal transduction must maintain fidelity and decrease noise while amplifying the signal. So the solution cannot be explained in terms of tightly bound, enduring molecular complexes, because the signals could not then be turned off. Rather, it seems to lie in first assembling weak binary complexes, and then using cooperative interactions to produce multi-component complexes in which the weak interactions are replaced by much stronger and more specific interactions.
    Although weak, nonspecific, transient complexes could give rise to a noisy system, such ‘encounter complexes’ might be exploited so that interaction partners do not have to be found afresh in the busy milieu of the cell, thus increasing the rate of formation of specific binary and higher-order complexes. Essentially, the partners bump into one another and are held loosely, allowing them time to become reorientated and repositioned on the surface or to adjust their shape to fit together more tightly. Recent studies are beginning to describe the dynamics of the assembly processes and to show that nonspecific, transient collisions play an important role in macromolecular associations.”

    How this is accomplished is discussed in more detail in the paper. Sounds a bit like electrical robots in a random dance that, on average, brings partners together with the right chemistry such that they get a brief charge out of the bond before trying other players.

    4. Trigger finger: There’s a chaperone in some bacteria called “trigger factor.” This machine was discussed by Ada Yonah in Nature 11/23,4 summarizing a couple of papers in the issue. He pictured it like a clamshell that attaches to the exit tunnel of the ribosome. As a nascent polypeptide emerges, there is a risk that the hydrophobic amino acid residues, like magnets, will stick to the wrong stuff in the cell and create a tangled mess. The trigger-factor clamshell forms a shelter around the exit tunnel, watching for these hydrophobic residues. When one pops out, it gloms onto it and lets go of the ribosome, protecting it from the intercellular medium, until the polypeptide can fold properly into its finished shape. The next trigger-factor chaperone takes its place on the exit tunnel for the next hydrophobic residue. When folding proceeds, the clamshell opens up and goes back to the exit tunnel to look for more. There’s an excess of trigger factor chaperones at all times. “This means that there is a continuous supply of trigger factor to protect a nascent chain,” Yonah explains.

    5. Not a simple needle prick: Two biologists described the “needle-nosed pump” known as Type-3 Secretion System (T3SS) in the Nov 30 issue of Nature.5 Though this machine, composed of 20 protein parts, shares some components with the famous bacterial flagellum, the authors did not dwell on this relationship but explained what else is known so far about T3SS. For one thing, it is much more complex than previously realized. Though it resembles somewhat a hypodermic syringe, the protein cargo it delivers is not just a needle prick into the host. A complex delivery channel is assembled at the tip. Moreover, assembly of the basal body and needle complex follows elaborate feedback mechanisms; the length of the needle complex is specifically controlled by either a “measuring cup” in the C-ring basal complex, or a “molecular ruler” in the channel or some other control method, such that the tip does not grow too long or too short. The machine also has to be built to the right diameter such that the substrate protein can pass through.
    The T3SS is implicated in many pathogenic bacteria, like Yersinia pestis, bubonic plague. Bacteria seem able to mimic the function of host proteins with substrates that function similarly without sequence similarity. Though the authors attribute this to “convergent evolution,” they open the possibility that the needle shots these bacteria give to eukaryotic cells can be beneficial. Why would bacteria mimic the legitimate proteins in a host? The authors say, “this strategy seems appropriate to have been adapted by bacteria that have type III secretion systems as a central element for the establishment of a close functional interface that is often symbiotic in nature.”
    Much remains to be learned about T3SS. The authors seem genuinely excited about the potential for understanding disease transmission and bacterial-eukaryote interactions through the continued elaboration of these molecular mechanisms. The 3-D diagrams look like something manufactured in a machine shop. The authors seem to think machine language is the appropriate code for describing them; they called these things “machines” 42 times. Let their ending paragraph express their enthusiasm:

    “The discovery of type III secretion machines has arguably been one of the most significant discoveries in bacterial pathogenesis of the past few years. The widespread distribution of such a macromolecular machine and its use in rather diverse biological contexts is a testament to the success of the evolutionary forces working to shape the complex functional interface between pathogenic or symbiotic bacteria and their eukaryotic hosts. Its central role in the interaction of many pathogenic bacteria opens up the possibility of developing new anti-infective strategies. In addition, a detailed understanding of these machines is allowing them to be harnessed to deliver heterologous proteins for therapeutic or vaccine purposes. The past few years have seen a rather remarkable increase in the understanding of these machines. There is no doubt that the importance and intrinsic beauty of these fascinating machines will continue to attract the attention of scientists and therefore progress is likely to continue at an even faster pace.”

    6. Centriole olé: Tiny devices called centrioles are vital to all life, because they duplicate each cell division and are intimately involved in it: “Centrioles are necessary for flagella and cilia formation, cytokinesis, cell-cycle control and centrosome organization/spindle assembly,” wrote 5 biologists in Nature 11/30.6 How the little machines duplicate themselves has been unclear. “Here we show using electron tomography of staged C. elegans [roundworm] one-cell embryos that daughter centriole assembly begins with the formation and elongation of a central tube followed by the peripheral assembly of nine singlet microtubules,” they announced. Various other proteins trigger, regulate, signal and terminate the process.
    Their models of the centrioles resemble cylinders lined by equally-spaced rods on the outside. The shape can be discerned in the photographs. “The structure of centrioles is conserved [i.e., unevolved] from ancient eukaryotes to mammals,” they noted, saying also at the end of the paper, “It is therefore likely that some of the assembly intermediates uncovered here in C. elegans are conserved in mammals and other eukaryotes.”
    As they reproduce, the daughter centrioles grow at a perpendicular angle to the mother. How this all happens is mysterious, but you can watch movies of these geometric structures emerging out of the cell matrix in the supplementary materials of the paper. The authors superimpose models of the centrioles to aid the visualization of a mechanical process just now coming into focus. To watch machinery 400 billionths of a meter in size assembling itself in a living cell is a harbinger of exciting days ahead for cell biology. For more on the lab roundworm C. elegans, visit our 06/25/2006 entry, and try counting the number of times “information” is used.

    7. Spectacrobatics: Three scientists from U of Maryland, publishing in PNAS7, employed a dramatic word rarely seen in a scientific paper while trying to figure out the interactions of another famous chaperone, the GroES-GroEL complex. They described a particular flip of a helix in the enzymes as “spectacular.” They used the word not only in the abstract but in the body of the paper, and added a synonym for emphasis. A coordinated switch between a network of salt-bridges in the enzyme produced what they called a “dramatic” outside-in movement. Must be quite a show. Now playing in a cell inside you.

    8. Dynein truckers: In the film Unlocking the Mystery of Life, Michael Behe spoke of molecular trucks that carry cargo from one end of the cell to the other. One of these trucks has a motor called dynein. To show that Behe was not exaggerating, read a press release on EurekAlert. It tells how a team of scientists U of North Carolina School of Medicine tried to figure out the power stroke of these little engines. In describing the way the enzyme exerts mechanical force by converting chemical energy (in the form of ATP) into mechanical energy, they also used the transportation metaphor. The article says, “the dynein puzzle is similar to figuring out how auto engines make cars move.” One of the researchers continued, “You have an engine up front that burns gas, but we didn’t know how the wheels are made to move.”
    What’s interesting is that the gas tank is quite a ways from the wheels; that means that the chemical energy must be transmitted over a substantial distance from where the power stroke actually occurs (if you consider a few nanometers a substantial distance). The truck is a speedster, too: “We saw it could allow a very rapid transduction of chemical energy into mechanical energy,” he said. That’s good, because there’s nanotons of work for a trucker in Cellville. “Conversion to mechanical energy allows dynein to transport cellular structures such as mitochondria that perform specific jobs such as energy generation, protein production and cell maintenance. Dynein also helps force apart chromosomes during cell division.” So the truck has as a good winch, too.
    These results were published in PNAS.8 Search on dynein above for more facts about these heavy lifters of the cell world, especially 02/25/2003 and 02/13/2003. Also interesting are the entries from 12/02/2004 and 04/13/2005. But then, 07/12/2004 might just blow you away.
    Speaking of Wired, the pop-technology website actually posted a story recently called “Mother Nature’s Nanotech.” Click here to see examples of cells that “will work for food.” Why reinvent the wheel? “Nature has everything nailed down already. Single-celled organisms are everywhere, and some slave-driving scientists have figured out that if you hitch ’em to microdevices and nanocargo, these bugs can be dragooned into doing all kinds of work. It’s time to domesticate the microworld. Mush, you Escherichia coli! Mush!” (See 09/06/2006).
    --------------------------------------------------------------------------------
    1Toren Finkel, “Cell biology: A clean energy programme,” Nature 444, 151-152 (9 November 2006) | doi:10.1038/444151a.
    2Helen Pearson, “Genetic information: Codes and enigmas,” Nature 444, 259-261 (16 November 2006) | doi:10.1038/444259a.
    3Tom L. Blundell and Juan Fernandez-Recio, “Cell biology: Brief encounters bolster contacts,” Nature 444, 279-280 (16 November 2006) | doi:10.1038/nature05306.
    4Ada Yonah, “Molecular biology: Triggering positive competition,” Nature 444, 435-436 (23 November 2006) | doi:10.1038/444435a.
    5Jorge E. Galan and Hans Wolf-Watz, “Protein delivery into eukaryotic cells by type III secretion machines,” Nature 444, 567-573 (30 November 2006) | doi:10.1038/nature05272.
    6Pelletier et al, “Centriole assembly in Caenorhabditis elegans,” Nature 444, 619-623 (30 November 2006) | doi:10.1038/nature05318.
    7Hyeon, Lorimer and Thirumalai, “Dynamics of allosteric transitions in GroEL,” Proceedings of the National Academy of Sciences USA, published online before print November 29, 2006, 10.1073/pnas.0608759103.
    8Serohijos et al, “A structural model reveals energy transduction in dynein,” Proceedings of the National Academy of Sciences USA, published online before print November 22, 2006, 10.1073/pnas.0602867103.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  2. #47
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    Mutations Accelerate Each Other’s Damage 12/14/2006
    As reported in our 10/14/2004 entry, mutations do not work in isolation; even the good kind usually conspire against the host. This fact has been largely ignored by neo-Darwinists. Some researchers at the Weizmann Institute in Rehovot, Israel, writing in Nature,1 tested the interaction of mutations (epistasis) on proteins. They found, in short, that harmful mutations usually accelerate the loss of fitness above what would occur in isolation. Some organisms exhibit robustness against mutations, though, as in well-known cases of antibiotic resistance. The team tested the robustness of E. coli while mutating a gene for a lactamase (TEM-1) that confers some resistance to ampicillin. They found that, at best, the organisms could hold out at a threshold level of fitness only temporarily. Beyond the threshold, death was speedy and inevitable. This was even after they removed the bad mutations:

    “Subjecting TEM-1 to random mutational drift and purifying selection (to purge deleterious mutations) produced changes in its fitness landscape indicative of negative epistasis; that is, the combined deleterious effects of mutations were, on average, larger than expected from the multiplication of their individual effects. As observed in computational systems, negative epistasis was tightly associated with higher tolerance to mutations (robustness). Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.”

    Their study also casts doubt on the ultimate survivability of so-called “neutral” mutations. These initially have no obvious effect on the fitness of the organism. This may be due to backup copies of a gene, suppressors of the mutated gene, and other mechanisms the cell uses to mask the damage. Eventually, however, the threshold is exceeded and the system collapses just as rapidly as a cell toppled by interacting harmful mutations.
    The authors of this study gave no indication that beneficial mutations can add up and help an organism. In fact, they failed to say anything about evolution that would provide hope for progress. By contrast, they offered a “new model” that sounds distinctly anti-evolutionary: cells are programmed to hold off the damage of mutations as long as they can, but will ultimately collapse under a mutational load. They concluded that “proteins may not be as robust as is generally assumed.” Their real-world experiment on bacteria showed robustness to mutations only to a certain point, then everything raced downhill:

    “Thus, theory and simulations have predicted a tight correlation between robustness and epistasis. Our work provides an experimental verification of this correlation and proposes a mechanism that accounts for it. Our model implies that any biological system that exhibits threshold robustness, or redundancy robustness, is inevitably epistatic. In such systems, mechanisms that purge potentially deleterious mutations, such as recombination (through sexual reproduction and other mechanisms) are of crucial importance, as they help to maintain this threshold. In this way, recombination, threshold robustness and negative epistasis may be interlinked—each being an inevitable by-product of the other.”

    They seem to be saying not only that mutations are not sources of positive fitness gains, but other proposed mechanisms like recombination are only stopgap measures to protect against the death spiral that would result when “randomly drifting proteins” gang up (negative epistasis) to cause a terror attack in the organism.
    --------------------------------------------------------------------------------
    1Bershtein et al, “Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein,” Nature 444, 929-932 (14 December 2006) | doi:10.1038/nature05385.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  3. #48
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    Animal Plan IT 12/15/2006
    Imitating animal technology is one of the hottest areas in science. The engineering and information technology (IT) observable in living things continues to astonish scientists and makes engineers want to imitate nature’s designs. Biomimetics is leading to productive, useful discoveries helping solve human problems and leading to a better life for all. Here are some recent examples of how scientists are working to reverse-engineer technical feats on the Animal Plan Net:

    Underwater jet propulsion lab: Squid know how to maneuver in ways that are the envy of submarine operators. That’s why researchers at U of Colorado are trying to imitate the “vortex ring” method of propulsion, according to Live Science. “Vortex rings are formed when a burst of fluid shoots out of an opening, moving in one direction and spreading out as it curls back.” If mastered, this technology might not only help underwater exploration subs, but permit the designing of microscopic craft that “guide tiny capsules with jet thrusters through the human digestive tract, enabling [doctors] to diagnose disease and dispense medications, the researchers said.”

    Skin so shiny: The octopus and its relatives, cuttlefish and squid, have an unusual skin that is perfect for camouflage, reports News@Nature. A group at Woods Hole, Massachusetts found a protein with “remarkable properties” that is responsible: it reflects light almost perfectly. Roger Hanlon found that the bottom layer of octopus skin is made up of cells called leucophores “composed of a translucent, colourless, reflecting protein” that has such perfect broadband reflection, “they reflect all wavelengths of light that hit at any angle.”
    Cuttlefish have an additional trick. Their leucophores are covered by flat platelets called iridophores that enhance “the brightness of the whiteness,” Hanlon said, adding, “These are very complex 3-D cells.” The protein involved is appropriately named reflectin.
    Reporter Katherine Sanderson explained how this knowledge can help humans. “The molecules that make octopus skin so successful as a dynamic camouflage could provide materials scientists with a new way to make super-reflective materials.” Such knowledge would be of interest to law enforcement and the military. Not only would this protect those working at night; some day, a Halloween costume made of cuttlefish skin could look pretty scary.

    Too cool watercraft Jet skis are going to seem like kid stuff when “Dolphin watercraft” become popular. Look at the picture on CNet News. The high-performance, submersible Dolphin can leap above the waves and do barrel rolls, just like a dolphin. Are these for real? Believe it or not; Innespace Productions has a website and picture gallery.
    The boats really do look like dolphins and come in one-person and two-person versions. Designers Dan Innes and Rob Piazza explain the principle: “These positively buoyant vessels use their forward momentum and the downward lift of their wings to literally fly below the water’s surface. This radical departure from the typical method of sinking below the surface allows the Dolphins to achieve an unparalleled level of freestyle performance.”
    As a result of their mimicry wizardry, their “fully functional show ready watercraft” is able to “perform sustained dives, huge jumps, barrel rolls, and many other amazing acrobatic tricks.” After their upcoming 2007 Dolphin demonstration tour, everybody will want one. Will this be the next competitive sport? Maybe someday Sea World will have live dolphins and their trainers in Dolphin watercraft competing side by side for audience applause. (If the inventors can get theirs to eat fish and reproduce, then they’ll really be onto something.)

    [b]Bug in a fix: Microbes may not be animals per se, but they also have technical secrets to teach us big animals. A deep-sea microbe at a scorching hot vent figured out how to fix nitrogen at a record temperature, 92°C, reported Science Daily and News@Nature. Though both articles speculated on how this new form of nitrogen fixation might have evolved, the feat has chemists interested in learning “to better mimic the process for industrial use.” Current artificial methods of fixing nitrogen to produce fertilizer are costly and inefficient compared to the way microbes do it. News@Nature quoted a French scientist saying, “Given the importance of nitrogen fixation in global agriculture and the creative exploitation of novel organisms by the biotechnology industry, a heat-stable nitrogenase is likely to find a useful industrial application.”

    Robo-flagellum: Live Science reported that somebody is already trying to mimic the bacterial flagellum. An Australian inventor has achieved higher rpm with less twisting force by imitating the way bacteria swim. Some day, his tiny inventions may be able to swim through your blood vessels, hopefully for beneficial ends: “Ultimately, tiny microrobots would give surgeons the ability to avoid traumatic and risky procedures in some cases,” Bill Christensen reported. “A remotely-controlled microrobot would extend a physician’s ability to diagnose and treat patients in a minimally invasive way.” Imagine surgery without scalpels and anesthesia. Could we see a day where you get surgery at an outpatient clinic, and watch a microbot in real time on a monitor screen as it swims on command inside you to the problem area with a load of medicine? It tickles just thinking about it.

    Question: would a lab technician be able to tell which entity running under flagellum power in a human bloodstream was intelligently designed, and which one evolved by chance over millions of years?

    If so, fire him for incompetence. Even a real dolphin could tell that a high-performance watercraft had to be intelligently designed. Don’t even ask the inventors unless you want to get slugged. The Dolphin boat didn’t just “emerge” by chance in their machine shop. They made it on porpoise.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  4. #49
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    Cell Zippers, Linemen and Editors Put on a Show 12/28/2006
    The golden age of cell biology continues. Scientists keep unlocking the secrets of cellular machinery with newer and better techniques. With the curtain rising on a show we could not previously imagine, played out on a stage so small it took centuries of scientific work to even see it, biochemists are discovering amazing tricks that the little autonomous actors have been performing all along, right inside of us.

    Zip me up, road crew: A press release on EurekAlert pointed to a new paper in Cell1 where researchers found a kind of monorail zipper. The original paper by Kikkawa and Metlagel actually calls it a “molecular ‘zipper’ for microtubules.” The EurekAlert article discusses “Roadworks on the motorways of the cell.” Cellular highways are 3-D monorails that run in all directions and are constantly being formed and recycled. Composed of protein units of tubulin, they first form into sheets that fold into a tube shape. That’s where Mal3p comes in. This little protein zips up the edges of the tube, forming a stable structure that would otherwise unravel easily. The zipper even forms an alternate trackway for the molecular “trucks” that use the microtubules to deliver goods all over the cell (12/04/2003, 02/25/2003, 07/12/2004).

    Mr. Goodwrench, the inchworm: DNA is tightly compacted in the cell, but needs to be unwound frequently for translation and duplication. A family of machines called helicases unwind the double helix as part of the process. Scientists wondered how the machine travels up and down the helix, and have now found that one particular helicase named UvrD both twists and jumps in a two-part power-stroke. The authors of another paper in Cell2 describe this as a “wrench-and-inchworm” mechanism. Each step, which traverses one DNA base at a time, requires two ATP fuel pellets. See also 06/19/2003, 01/05/2006, bullet 9, and 10/27/2005, bullet 3; see 01/19/2005 about an RNA helicase.

    Not many typos get past this editor: Life depends on 20 specialized translators that connect the DNA code to the protein code (see 09/16/2004 for historical background, and 06/09/2003 and its embedded links for conceptual background). The awkwardly-named “aminoacyl-tRNA synthetases” (AARS for short) are highly specialized to connect the two codes correctly and edit out mistakes before they cause serious trouble. A paper in PNAS3 discussed one of the ways the AARS for the amino acid phenylalanine works. For jargon lovers, the model is: “the role of the editing site is to discriminate and properly position noncognate substrate for nucleophilic attack by water.” To test the model, they tinkered with some of the pieces of the protein machine and watched the editing precision drop dramatically. The precision of the active site is part of the “translational quality control,” they said (see 12/20/2003, 09/09/2002).

    Oxygen can be bad for your health: We like to breathe in that oxygen, but in the wrong places it can be a poison. Authors of another paper in PNAS4 found that “oxidized messenger RNA induces translation errors.” They put the gene for the light-glowing protein luciferin into rabbits (imagine a glowing Bugs Bunny) in both oxidized and non-oxidized forms. Although the oxidized translation machine stayed intact, the “translation fidelity was significantly reduced.”

    How could such precision translation machinery evolve? A paper in Structure,5 another Cell Press journal, bravely investigated the evolution of the genetic code (see 11/01/2002 for a previous attempt). They understood the requirement for high fidelity:

    “This specificity is critical for the accuracy of the genetic code, which has to be maintained to the highest degree to prevent mistranslation, that is, incorporation of the wrong amino acids at specific codons.”

    They tried to envision the transition from a hypothetical “RNA world” (07/11/2002) of miscellaneous floating ribozymes to the DNA-mRNA-tRNA-protein system now universally employed in all living things. That’s no small order. It requires a good imagination, as their introduction makes clear:

    “Since the discovery of ribozymes and the development of the idea of life first emerging from an RNA world (Gilbert, 1986), biologists have struggled to imagine the logical progression of events that led to proteins. At the same time, regardless of what the imagination can conjure, a connection to reality has to be made. That, in turn, requires experiments to test specific hypotheses or to provide an opportunity for serendipitous findings.
    To go from RNA to proteins requires the genetic code—triplets of nucleotides representing single amino acids. The modern code is an algorithm determined by aminoacylation reactions, whereby each of 20 amino acids is linked to its cognate tRNA that bears the anticodon triplet of the code. The 20 aminoacyl tRNA synthetases (one for each amino acid) that catalyze these reactions are ancient proteins that were present in the last common ancestor of the tree of life (Carter, 1993 and Cusack, 1997). As the eons passed, the tree split into the three great kingdoms—archaea, bacteria, and eukarya, which encompass all life forms. Yet, the genetic code remained fixed, with the same 20 aminoacyl tRNA synthetases making the same connections between anticodon triplets and amino acids. Thus, clues to the history of the transition from the RNA world to proteins might be imbedded in the tRNA synthetases themselves.”

    The best they could do was to suggest that a few of the aminoacyl-tRNA-synthetases hold hints of a prior RNA-ribozyme ancestry. Three of them, for instance, perform the editing while gripped to the transfer RNA (tRNA), resembling a “ribonucleprotein” that might have been the successor to the initial ribozymes in the RNA soup. The words might, may and perhaps were evident in their article, however. These speculative words looked pretty stark next to the clear evidence of precision in the translating machinery. The AARS for glutamine, for instance, is able to distinguish between four very similar-looking molecules and pick the right one. A conformational change in the binding pocket kicks out the interlopers and makes sure the correct amino acid gets attached to the tRNA. Their conclusion, therefore, seemed to make a giant leap of faith:

    “Thus, what is reported in this most recent work on GluRS—that a synthetase can use tRNA to direct a conformational change that perfects amino acid specificity, using in part a contact with the tRNA itself—may provide a general mechanism of tRNA-dependent amino acid specificity. The much bigger implication is that perhaps this functional interaction is a picture or a “holdover” from an earlier era in the evolution of the genetic code.”

    --------------------------------------------------------------------------------
    1Kikkawa and Metlagel, “A molecular ‘zipper’ for microtubules,” Cell, Volume 127, Issue 7, 29 December 2006, Pages 1302-1304.
    2Lee and Yang, “UvrD Helicase Unwinds DNA One Base Pair at a Time by a Two-Part Power Stroke,” Cell, Volume 127, Issue 7, 29 December 2006, Pages 1349-1360.
    3Ling, Roy and Ibba, “Mechanism of tRNA-dependent editing in translational quality control,” Proceedings of the National Academy of Sciences USA, published online before print December 21, 2006, 10.1073/pnas.0606272104.
    4Tanaka, Chock and Stadtman, “Oxidized messenger RNA induces translation errors,” Proceedings of the National Academy of Sciences USA, published online before print December 26, 2006, 10.1073/pnas.0609737104.
    5Schimmel and Yang, “Perfecting the Genetic Code with an RNP Complex,” Structure, Volume 14, Issue 12, December 2006, Pages 17291730.

    Hope you enjoyed this another peek into cellular wonders. We had to throw in an evolutionary tale just for the sheer contrast of seeing actual scientific investigation into observable machinery operating with high fidelity and quality control juxtaposed against the speculations of certain humans forced by their worldview to imagine that it just happened by chance. You can see what they’re up against.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  5. #50
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    This Bacterium Moves Like a Tank 01/03/2007
    Mark McBride (U of Wisconsin) has been trying for a decade to figure out how a gliding bacterium glides. His conclusion: the microbe has tire treads like a conveyor belt that make it roll over a variety of surfaces, like an all-terrain vehicle.
    According to a U of Wisconsin press release, the Department of Energy (DOE) is interested in this bacterium, Cytophaga hutchinsonii, because it can digest paper and other forest by-products. This is the first step in converting biomaterial into ethanol, to use as fuel.
    Of the cell’s “parts list,” McBride identified 24 genes involved in its gliding motility. He attached tiny latex spheres to the cell surface and then watched them move in all directions. “The cell wall appears to have a series of moving conveyer belts,” he said. He described these nearly invisible filaments as like tire treads, “designed to help the organism move over a variety of surfaces, like an all-terrain vehicle.” He believes these structures also convey cellulose into the interior of the cell, toward specialized organelles that digest it.
    Figuring out how this cell digests cellulose is still a work in progress. Unlike other bacteria that know the trick, this one “may use either a novel strategy or novel enzymes.” The Department of Energy is interested in this research. It may help our energy-hungry civilization “find other renewable materials that will be cost-effective alternatives, such as paper pulp, sawdust, straw and grain hulls.”
    What really intrigues McBride about his research on C. hutchinsonii, though, is what makes it go. He and his students have been comparing it with another gliding bug, Flavobacterium johnsoniae, that although “not closely related,” may “use the same basic machinery to move.” How different are these two? McBride claimed, “You are more closely related to a fruit fly than these two organisms are to each other.”
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  6. #51
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    Cells Use Zip Codes to Determine Their Body Location 01/13/2007
    Scientists reported in an article in PLOS1 that cells have the equivalent of a Zip-code built in to their DNA that codes their location in the body. Skin cell DNA from 47 locations on a subjects were compared. Three locations on the DNA were found to correspond to the location of the cell in the body, specifying whether it came from the upper or lower torso, near to or far from to the center of the body, and near to or far from the surface of the body. How cells know where they are in the body has always been a puzzle, and now it turns out the cell address is coded into the DNA:

    "A major question in developmental biology is, How do cells know where they are in the body? For example, skin cells on the scalp know to produce hair, and the skin cells on the palms of the hand know not to make hair. Overall, there are thousands of different cell types and each has a unique job that is important to overall organ function. It is critical that, as we grow and develop, each of these different cells passes on the proper function from generation to generation to maintain organ function. In this study, the authors present a model that explains how cells know where they are in the body. By comparing cells from 43 unique positions that finely map the entire human body, the authors discovered that cells utilize a ZIP-code system to identify the cell?s position in the human body. The ZIP code for Stanford is 94305, and each digit hones in on the location of a place in the United States; similarly, cells know their location by using a code of genes. For example, a cell on the hand expresses a set of genes that locate the cell on the top half of the body (anterior) and another set of genes that locates the cell as being far away from the body or distal and a third set of genes that identifies the cell on the outside of the body (not internal). Thus, each set of genes narrows in on the cell?s location, just like a ZIP code. These findings have important implications for the etiology of many diseases, wound healing, and tissue engineering."

    --------------------------------------------------------------------------------
    1 Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY (2006) Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs. PLoS Genet 2(7): e119 DOI: 10.1371/journal.pgen.0020119
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  7. #52
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    Cell Membrane Has Ticket-Operated Turnstiles 01/27/2007
    Cells are like castles surrounded by walls. A wall without gates, however, would prevent commerce and trap the inhabitants inside. The cell has ingenious gates that control the flow of goods and services through its outer membrane under tight surveillance and quality control. This controlled flow, as opposed to passive diffusion or osmosis, is termed active transport. Depending on the type of import or export required, the cell uses a variety of mechanisms. It might wrap the cargo in clathrin proteins and send it through in a self-mending breach of the walls (endocytosis; 05/15/2005, 11/04/2005, bullet 7). It might use one of the specialized authenticating channels through the membrane (e.g., aquaporins 04/18/2002 and ion channels, 05/29/2002). It might export genetic material or proteins through one of the pumps, or secretion systems (10/11/2005, 11/10/2004). Or, it might check cargo through one of the varieties of self-operating ticketed turnstiles.
    A description of one of these gates excited awe in a commentary in PNAS.1 Robert M. Stroud summarized decades of work on a kind of lactose turnstile. Key researcheers published their latest results in the current issue of the journal. They believe they have finally figured out how this molecule-sized machine works. It is a protein, 417 amino acids long, folded into a kind of rocking turnstile in the membrane. For a lactose passenger to get through the membrane using this transporter, it has to pay the fare. A proton must first be inserted into the active site. Then, the lactose molecule gets in and fastens its seat belt, so to speak. The nanomachine then undergoes a conformational change that seals off the outside and opens the door to the inside, where the passengers undock. Then, the gate automatically repositions itself for the next load. Called LacY, or lactose permease, this molecular machine operates with practically 100% efficiency: each proton ticket grants admittance to one and only one lactose passenger.
    LacY is one of a whole family of gates called the “Major Facilitator Superfamily” (MFS).2 “The mechanism most probably pertains to the many other transporters of the MFS that are found throughout all domains of life,” Stroud says. Another member of this family, for instance, is called the GlpT. This machine works with a reverse-ticketing process; a phosphate outside the cell is exchanged for a glycerol phosphate inside.
    Stroud was palpably delighted with the elucidation of the mechanism of these intriguing machines after so much research for many years. Here’s what he said about the LacY device:

    “The MFS of transporters can be run in reverse, such that outward movement of lactose, driven by reverse concentration gradient, can generate an H+ gradient across the membrane; LacY can work in either direction toward a coupled equilibrium. It is a beautiful example of energy transduction at the level of the membrane and is a near-perfect machine in the sense that the stoichiometry3 is always 1:1 without any leakage.”

    Leakage would allow contraband through. Experimental inventory shows all goods accounted for, before and after. The protein undergoes “large global conformational changes to transport the cargo” that are reversible, providing “oscillation between structural states that become accessible alternately to one side or the other, which can therefore be coupled to other sources of energy.”
    Understanding how these machines work could lead to treatments for diseases caused by their malfunctions, such as cystic fibrosis and lactose malabsorption, as well as to new methods for administering antibiotics and chemotherapeutic drugs.
    --------------------------------------------------------------------------------
    1Robert M. Stroud, “Transmembrane transporters: An open and closed case,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610349104, published online before print January 24, 2007.
    2Another superfamily of transporters, the ATP Binding Cassette (ABC) family, is driven by ATP hydrolysis inside the cell.
    2Stoichiometry refers to the ratios of combining elements in a chemical reaction, from the Greek stoichea, “basic principles,” as used in Colossians 2:8.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  8. #53
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    Muscles Use Gears, Automatic Transmission 01/28/2007
    Analogies may not be perfect representations of reality, but it must pique the interest of all of us the way Elisabeth Pennisi in Science1 compared muscle to cars and bicycles:

    “One look at a ballerina as she pirouettes and poses drives home the remarkable ability of our muscles to adapt to diverse biomechanical demands. Manny Azizi and Thomas Roberts, biomechanists at Brown University, have now found that as certain muscles contract, they vary their shape to balance the need for speed and force. It’s as if these muscles have a builtin automatic transmission, says Azizi....
    [Azizi’s] simulations showed that certain muscle shapes caused contracting pinnate fibers to shift to a less steep angle. When that happens, the muscle’s overall height decreases more than it would have had the fibers maintained their angle. In other words, the virtual muscle shifted into the equivalent of a high gear ratio, increasing the speed of contraction.... Azizi then looked at whether real muscles acted this way. He had expected that each pinnate muscle would have just one gear ratio, that is, undergo a characteristic shape change, and therefore be strong or contract fast but not have both features.... [they found] the muscle operated at a lower gear and took full advantage of the dense packing of pinnate fibers....
    Just as one changes gears on a bicycle to crawl up an ever-steeper hill, “the direction of change in the muscle gears matches the mechanical demands of contraction,” Azizi said. Moreover, the muscle’s shifting of gears required no nervous system input, occurring automatically depending on the load applied.”

    Imagine--your muscles are like a bicycle with automatic transmission. The gearbox of muscle surprised the researchers. “A single muscle undergoes not one shape change but a range of different shape changes under different circumstances,” Azizi found. While pinnate muscles can rotate under light loads, they are prevented from rotation under heavy loads by the pull on the fibers. “Thus, although pinnate muscles are supposedly specialized for force, under light demand, they can also work fast,” Pennisi explained. A colleague admired this study “assessing muscle architecture with relation to function.”
    --------------------------------------------------------------------------------
    1Elisabeth Pennisi, “News Focus: SOCIETY FOR INTEGRATIVE AND COMPARATIVE BIOLOGY MEETING: Muscle Fibers Shift Into High Gear,” Science, 26 January 2007: Vol. 315. no. 5811, p. 456, DOI: 10.1126/science.315.5811.456b.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  9. #54
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    Cell Quality Control Runs a Tight Ship 01/31/2007
    Without the surveillance and rapid response of quality control, cells would collapse and die. Here are some recently-published examples of nanoheroes in action.

    Plant checkpoints: Picture a child watching the wonder of a seedling breaking through the soil into the light for the first time. Within hours, the ghostly-white stem turns green, and a day later, leaves begin to appear. Does he or she have any idea what is going on at a scale too small to see? Not until that kid grows into a modern lab scientist with sophisticated equipment. The transformation requires the coordinated transportation of key elements through specialized checkpoints, an international team reported in PNAS.1
    Without boring the reader with technical terms, what basically happens is this. The underground seedling contains pre-chloroplast parts in readiness for the arrival into sunlight, but saves its energy by not allowing the light-gathering factories to assemble until it’s time. “Chloroplasts need to import a large number of proteins from the cytosol because most are encoded in the nucleus,” they reported. Once there, they have a double membrane to get through. Specialized gates permit entry of the authenticated parts. One particular light-sensitive part has its own unique gate. The team decided to see what happened when they mutated one gene in the process. The results were not pretty: the light-sensitive molecules accumulated outside the plastid because they couldn’t get into the factory. “After a dark-to-light shift, this pigment operated as photosensitizer and caused rapid bleaching and cell death,” they found. “Our results underscore the essential role of the substrate-dependent import pathway” that this protein depends on. Maybe this error resembles a chemical spill outside a pharmaceutical plant, or pistons firing before they get into the engine.

    Now hear this: In a surprise finding that might provide hope for the deaf, scientists publishing in PNAS reported that “Restoration of connexin26 protein level in the cochlea completely rescues hearing in a mouse model of human connexin30-linked deafness.”2 Two protein partners are needed for healthy hair-cell formation in the cochlea of the inner ear. Mutations in one of them, connexin26, account for about half of all cases of inherited human deafness. Usually, connexin26 and connexin30 join together to form gap junctions, but if one is mutated, deafness results. The gap junctions are essential for cell-to-cell communication. Surprisingly, connexin26 (Cx26) appears able to bridge the gap when connexin30 (Cx30) is missing; therefore, “up-regulation of Cx26 or slowing down its protein degradation might be a therapeutic strategy to prevent and treat deafness caused by Cx30 mutations.”
    The scientists suspected that these two isoforms of connexins regulate each other. They also noted that this partnering occurs in the lens of the eye. Losing one by mutation, therefore, affects the regulation of the partner. On a hunch that one of the isoforms could compensate for the loss of the other if allowed to assemble, and could build functional gap junctions on its own, they tried up-regulating the remaining connexin. To their surprise, hearing was completely restored in mice.

    Bad translator triggers SOS: We’ve talked about the DNA translation team a number of times (e.g., 12/28/2006, 07/26/2005, 06/09/2003, 04/29/2003). The team of 20 aminoacyl-tRNA synthetases, as they are called, have rigid requirements. “Mistranslation in bacterial and mammalian cells leads to production of statistical proteins that are, in turn, associated with specific cell or animal pathologies, including death of bacterial cells, apoptosis of mammalian cells in culture, and neurodegeneration in the mouse,” said Bacher and Schimmel in PNAS.3 “A major source of mistranslation comes from heritable defects in the editing activities of aminoacyl-tRNA synthetases.” This is because the protein machines, which snap the right amino acid onto the appropriate transfer-RNA (tRNA), cannot perform their vital role in protein synthesis if broken.
    These researchers suspected that broken synthetases could also cause mutations. They decided to test what happens when they caused an “editing defect” in one of them. (These enzymes are usually able to proofread their own errors with a high degree of accuracy.) The result, again, was not pretty: “A striking, statistically significant, enhancement of the mutation rate in aging bacteria was found.” The bug was like flipping a fire alarm: “This enhancement comes from an increase in error-prone DNA repair through induction of the bacterial SOS response,” they explained. “Thus, mistranslation, as caused by an editing-defective tRNA synthetase, can lead to heritable genetic changes that could, in principle, be linked to disease.”
    Another press release from Ohio State also discussed the neurological disease that can result from mistranslated proteins caused by mutated aminoacyl-tRNA synthetases.

    --------------------------------------------------------------------------------
    1Pollman et al, “A plant porphyria related to defects in plastid import of protochlorophyllide oxidoreductase A,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610934104, published online before print January 29, 2007.
    2Ahmad et al, “Restoration of connexin26 protein level in the cochlea completely rescues hearing in a mouse model of human connexin30-linked deafness,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0606855104, published online before print January 16, 2007.
    3Jamie M. Bacher and Paul Schimmel, “An editing-defective aminoacyl-tRNA synthetase is mutagenic in aging bacteria via the SOS response,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610835104, published online before print January 30, 2007.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  10. #55
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    Cells Perform Sporting Interactions 01/31/2007
    The components of living cells perform such acrobatic moving interactions, one would think they are having fun. Here’s the news from the Wide World of Cellular Sports.

    Speedway: A news release from Penn Medicine talks about how motor proteins step on the gas and the brakes in their motions around the cell. The announcer from the booth calls the action:
    “Imagine that the daughter microtubule is a short train on the track of the mother microtubule,” explains [Phong] Tran. “The molecular motor is the train’s engine, but the problem is that the cargo – the molecular brakes – gets longer, slowing down the daughter train. But when the train gets to the end of the track it remains attached to the end of mother microtubule. At the tail end, it stops moving and that defines the region of overlap. Our work shows that the cell can make microtubule structures of defined lengths stable by coordinating the sliding of the motors and the slowing of the brakes.”
    The press release contains videos of the speedway in action.

    Square Dance: Chromosomes line up in their territories like square dancers on cue, explained an article in Nature (1/25).1 They even use their arms: “In addition, the structure of the DNA within chromosome territories is nonrandom, as the chromosome arms are mostly kept apart from each other and gene-rich chromosome regions are separated from gene-poor regions. This arrangement probably contributes to the structural organization of the chromosome, and might also help in regulating particular sets of genes in a coordinated manner.”
    “Remarkably,” even the territories themselves “arranged in particular patterns within the nucleus,” the article explains. Here’s part of the choreography inside the dance hall (i.e., the nucleus):

    “In lower eukaryotes such as plants and flies chromosomes tend to be polarized, with the ends of the arms (telomeres) on one side of the cell nucleus and the point at which the two arms meet (the centromere) on the opposite side. In mammalian cells, however, chromosome arrangement is more complex. Even so, each chromosome can be assigned a preferential position relative to the nuclear centre, with particular chromosomes tending to be at the nuclear interior and others at the edge (Fig. 2a). This preferential radial arrangement also, of course, gives rise to preferred clusters of neighbouring chromosomes.”

    The players get to socialize, too: “Even the two copies of the same chromosome within the same nucleus often occupy distinct positions and have different immediate neighbours.” Each chromosome tends to hang out with partners in the same developmental pathways, though. “It seems that the actual position of a gene in the cell nucleus is not essential to its function,” the author writes. So, the interviewer asks, “Why have all this organization?” Is it just for fun? “It is more likely that positioning contributes to optimizing gene activity.” It also serves the time-honored strategy of networking:

    “The nonrandom organization of the genome allows functional compartmentalization of the nuclear space. At the simplest level, active and inactive genome regions can be separated from each other, possibly to enhance the efficiency of gene expression or repression. Such compartmentalization might also act in more subtle ways to bring co-regulated genes into physical proximity to coordinate their activities. For instance, in eukaryotes, the genes encoding ribosomal RNAs tend to cluster together in an organelle inside the nucleus known as the nucleolus. In addition, observations made in blood cells suggest that during differentiation co-regulated genes are recruited to shared regions of gene expression upon activation.”

    How each partner finds its spot, we don’t know. Somehow, they always find their way back:

    “Chromosomes are physically separated during cell division, but they tend to settle back into similar relative positions in the daughter cells, and then they remain stable throughout most of the cell cycle.”

    The author claims this behavior is “evolutionarily conserved” (i.e., unevolved).

    Baton race: Passing chemical tags without stumbling is described by a paper in Nature2 that opens, “Modifier proteins, such as ubiquitin, are passed sequentially between trios of enzymes, like batons in a relay race. Crystal structures suggest the mechanism of transfer between the first two enzymes.” As the tags get passed from group to group, the players sometimes undergo large shape changes to hold the tag properly. In one case, for instance, “combined conformational changes create a surface to which an E2 enzyme binds with high affinity.” These bends and rotations make the enzymes act like a “conformational switch” to turn on the next reaction in the chain, like handing off the baton.

    Capture the Flag: Another paper in Nature3 described how the cell cycle often depends on reading tags hidden on chromosomes. Describing the “intricate process” of this game, even describing the participants as “players,” a researcher from UC Berkeley calls the action:

    “Transitions between all cell-cycle phases are controlled by the activation and deactivation of a series of cyclin-dependent kinases (CDKs), which control the phosphorylation of other proteins.”

    Researchers were having a challenge following the flag. “Thus, after the origin-recognition complex had been identified, finding the actual targets for S-CDK, the CDK known to promote the switch from G1 to S phase, became a major objective.”

    Acrobatics and juggling: A paper in PNAS4 describes the dynamic motions of one enzyme that uses three metal ions and multiple conformational changes for precise action on its substrate. “It is evident that the trimetal cluster undergoes significant structural reorganization in the course of the reaction,” they wrote. Visualize this circus act as they describe it:

    “The analysis presented here emphasizes the significant level of complexity involved in enzymatic catalysis by multinuclear enzymes even when the underlying chemical transformation is relatively straightforward. At the same time certain universal patterns regarding the multiple mechanistic roles of the metal cofactors emerge. First, the metal ions play a role in generating the reactive nucleophile. This process involves precise positioning of a carboxylate ligand to deprotonate an exogenous water molecule and orient the resulting hydroxide for an in-line attack. Deprotonation is further facilitated by the combined electrostatic effect of two zinc ions (Zn1 and Zn2), necessitating a relatively close distance between them. The second role of the metals is to accommodate and electrostatically stabilize the more compact partly associative transition state. Hence, an overall contraction of the trimetal cluster is observed. Finally, a metal cofactor (Zn3) is responsible for stabilizing the developing charge on the leaving group toward the end of the reaction. To effectively carry out these roles, the active site rearranges dynamically, a finding, that underscores the crucial importance of flexibility for the reactive transition.”

    Since this enzyme is part of the DNA Repair Team, the participants probably don’t do it for applause or to be heroes. To them, it’s all in a day’s work.

    Human researchers seem to be joining in the games. Identifying the sports repertoire inside a cell is like a treasure hunt.
    --------------------------------------------------------------------------------
    1Meaburn and Misteli, “ Nature 445, 379-781 (25 January 2007) | doi:10.1038/445379a.
    2Trempe and Endicott, “Structural biology: Pass the protein,” Nature 445, 375-376 (25 January 2007) | doi:10.1038/nature05564.
    3Michael Botchan, “Cell biology: A switch for S phase,” Nature 445, 272-274 (18 January 2007) | doi:10.1038/445272a.
    4Ivanov, Tainer and McCannon, “Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV.” Proceedings of the National Academy of Sciences USA, doi 10.1073/pnas.0603468104, January 30, 2007, 104:5, pp. 1465-1470.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  11. #56
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    Cells Perform Nanomagic 02/13/2007
    The cell is quicker than the eye of our best scientific instruments. Biochemists and biophysicists are nearing closer to watching cellular magic tricks in real time but aren’t quite there yet. They know it’s just a trick of the eye, but it sure is baffling how cellular machines pull off their most amazing feats. Think, but don’t blink:

    Knot Wizardry: Proteins needing a fold go into a private dressing room (05/05/2003). The most glamorous and well-equipped room, the GroEL-GroES chaperone, helps the star emerge just right. How it does this is as puzzling as watching a magician untie a Gordian knot under a kerchief. There are thousands of wrong ways a protein could fold; how does the chaperone always perform the trick correctly? Some of the bonds between domains (disulfide bridges) are a long way apart. What brings them together, and what keeps the wrong bridges from forming?
    Some scientists at Howard Hughes Medical Institute, writing in PNAS,1 cheated and built the chaperone with one door open so they could peek inside. They still couldn’t figure it out completely. Something in the chaperone creates conditions that favor the correct “native” fold, but also fix the mistakes before the prima donna protein emerges. Somehow they do this without any ATP energy cost. “We conclude that folding in the GroEL-GroES cavity can favor the formation of a native-like topology, here involving the proper apposition of the two domains of TG [trypsinogen, the enzyme in the experiment]; but it also involves an ATP-independent conformational ‘editing’ of locally incorrect structures produced during the dwell time in the cis cavity.”

    Speed Solve: Maybe you’ve watched a blindfolded man solve a Rubik’s cube in seconds and wondered how it was done. You can imagine the bewilderment of German and Swiss scientists watching a protein fold in far less time. Protein chains of hundreds of amino acids have to explore a vast space of possible folds yet arrive at the one correct fold, often in fractions of a second. These scientists, writing in PNAS,2 used lasers to try to figure out in slo-mo how this happens.
    As with a Rubik’s cube, there are billions of ways a protein could fold incorrectly. Parts of a nascent protein chain form loops in the process of solving the puzzle. “Exponential kinetics observed on the 10 to 100-ns time scale [ns=nanosecond, a billionth of a second] are caused by diffusional processes involving large-scale motions that allow the polypeptide chain to explore the complete conformational space,” they said. “The presence of local energy minima [e.g., loops] reduces the conformational space and accelerates the conformational search for energetically favorable local intrachain contacts.” To catch these loops, they had to look fast. “Complex kinetics of loop formation were observed on the 50- to 500-ps [picosecond] time scale,” they noted. A picosecond is a trillionth of a second. Good thing they had lasers that could flash up to a femtosecond (quadrillionth of a second), or it would all be a blur.

    Levitation: With a feat better than defying gravity, “Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms,” wrote a Finnish team also publishing in PNAS.3 To do this trick, the enzyme has to go against the force.
    Scientists like to talk in dispassionate language, but they called this enzyme “remarkable,” so they must have liked the magic act. “This remarkable membrane-bound enzyme also converts free energy from O2 reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump,” they remarked about the remarkable. The way this pump works has “remained elusive,” even though most of the structure has been known. With special spectroscopic and electrometric techniques, they were able to observe the trick in real time. Abracadabra led to eureka: “The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties.” OK, tell us. What’s the secret?

    “The 10-microsecond electron transfer to heme [iron complex] a raises the pKa of a “pump site,” which is loaded by a proton from the inside of the membrane in 150 microseconds. This loading increases the redox potentials of both hemes a and a3, which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a3/CuB center, and the electron is transferred to CuB. Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.”

    So, there. Now you know the trick. Uh, how’s that again? Actually, they only figured out part of the trick; “some important details remain unsolved,” they confessed, “e.g., the identity of the proton-accepting pump site above the hemes.” Their diagram of the enzyme looks for all the world like magician’s tightly-cupped hands, with the active site secreted within. Maybe this could be dubbed sleight-of-enzyme.

    In the introduction to this last paper, the authors described how the enzyme is essential to all life. It is a key player in the transfer of electrons and protons that feed the ATP synthase motors that produce ATP – the universal energy currency for all living things. Water is produced in the process that generates oxygen (in plants) and consumes it (in animals). These reactions would not occur without the machinery to drive them against the physical forces of diffusion.
    The scientists are converging on a mechanical description of how the pumping action works. “Each of the four electron transfer steps in the catalytic cycle of CcO [cytochrome c oxidase] constitutes one cycle of the proton pump, which is likely to occur by essentially the same mechanism each time,“ they said. “Here, we report on the internal electron transfer and charge translocation kinetics of one such cycle, which is set forth by fast photoinjection of a single electron into the oxidized enzyme.”
    --------------------------------------------------------------------------------
    1Eun Sun Park, Wayne A. Fenton, and Arthur L. Horwich, “Disulfide formation as a probe of folding in GroEL-GroES reveals correct formation of long-range bonds and editing of incorrect short-range ones,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610989104, published online before print February 5, 2007.
    2Fierz, Satzger et al, “Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0611087104, published online before print February 6, 2007.
    3Belevich et al, “Exploring the proton pump mechanism of cytochrome c oxidase in real time,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0608794104, published online before print February 9, 2007.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  12. #57
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    Cell Calcium Channel: Meet Me at the Gate 03/16/2007
    All cells use calcium ions for signalling. The ions flow through specialized gates in the plasma membrane. Inside the cell, receptors line the endoplasmic reticulum (ER), a kind of subway system where finishing work on proteins is done. How do the two get together? They arrange a meeting.
    Richard Lewis, writing in Nature,1 describes how scientists found this out. It appears that the ER and the calcium channels talk to each other. When the ER is running low on calcium ions, a messenger molecule goes to the plasma membrane, and starts a process where the channels and a portion of the ER move independently toward a meeting point. The channels cluster to a spot on the membrane where a fold in the ER joins to meet it, and the calcium ions are delivered right to where they are needed. In Lewis’s words, “New findings reveal a unique mechanism for channel activation, in which the CRAC channel [calcium release-activated channel2] and its sensor migrate independently to closely apposed sites of interaction in the ER and the plasma membrane.”
    What are these processes good for? The short list includes: secretion, motility, gene expression, cell growth, and activation of the T cell response to antigens. This emerging picture comes after “years of frustration” looking for the mechanism by which this interaction worked. They finally found the secret using forward and reverse gene activation methods.
    In the paper, Lewis included a cartoon diagram of the play-by-play process. He called it a kind of “molecular choreography” in which the cell performs “assembly on demand”. Using the word “Remarkably” twice in the paper, he commented on the significance of this apparatus: “This kind of choreographic activation mechanism, in which a channel and its sensor migrate within distinct membranes to reach a common interaction site, is unprecedented.” But why don’t the receptor and channel just stay put in close proximity? It’s likely, he explains, that the oscillations in calcium activity introduce delays that create local signaling domains, enhancing the specificity of calcium signaling for particular purposes.
    The picture may be more complex than it looks already. The signaling proteins he described may be part of multi-protein complexes. Something, for instance, has to give the open sesame password to the channel. Other activators may be required to call the components to the rendezvous site.
    Lewis did not mention evolution in this paper, except to note twice that parts of the system are conserved (i.e., unevolved) from Drosophila (fruit flies) to humans. Since such vastly diverse organisms are composed of cells, and all cells employ calcium signalling, this probably implies the system is conserved throughout the eukaryotic kingdom if not all life.

    --------------------------------------------------------------------------------
    1Richard S. Lewis, “The molecular choreography of a store-operated calcium channel,” Nature 446, 284-287 (15 March 2007) | doi:10.1038/nature05637.
    2CRAC is unusual among the family of calcium channels. Lewis describes it: “The unusual characteristics of this channel have long intrigued ion-channel biophysicists; it selects for Ca2+ just as well as CaV channels but conducts Ca2+ >100 times more slowly, is inactivated by intracellular Ca2+ on timescales separated by three orders of magnitude, and requires extracellular Ca2+ to be fully active.” The reasons for these “unique channel properties” are still under investigation. It will take time to obtain a “global view of the molecular workings of store-operated channels and their physiological roles.” The overall effectiveness of the system in vital roles suggests there is a reason for its slow activation compared to other calcium channels.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  13. #58
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    Have Scientists Found the Secret of Aging? 03/17/2007
    There’s a tragic disease that speeds up aging. Known as progeria (Huntington-Gilford progeria syndrome, HGPS), it is caused by a single point mutation in exon 11 of the NMLA gene. Children afflicted with this disease look old beyond their years and often die at 13 of heart attack and stroke – essentially, of old age.
    A team of scientists at the National Institutes of Health (NIH), publishing in PNAS,1 investigated the results of this mutation.2 They found that the gene builds a mutant lamin-A protein named progerin/LA-delta-50 that lacks the cleavage site to remove a string of RNA during protein synthesis. As a result, when it comes time for the cell to divide, “During interphase, irreversibly farnesylated progerin/LA-delta-50 anchors to the nuclear membrane and causes characteristic nuclear blebbing” [i.e., bulging]. This causes “abnormal chromosome segregation and binucleation.”
    The NIH team followed up on a recent study that small amounts of the mutant protein are found in normal fibroblasts (cells that give rise to connective tissues, like collagen). They wondered if this is implicated in the normal aging process. We all have a tiny amount of this mutant protein, the studies suggest. Fortunately, anti-progerin antibodies monitor our connective tissues looking for giant nuclei and cells with two nuclei, and induce them to self-destruct (apoptosis).
    What appears to go wrong, though, is that some of the mutant cells get through the defenses. The team believes that there is some kind of “irreversible switch” in late-passage cells, allowing the cryptic splice to proceed, “initiating a series of events that lead to mitotic defects and ultimate senescence.” If this is true, we all have progeria. The unfortunate victims of HGPS just have a faster version. Here’s their conclusion:

    “In summary, our studies demonstrate the abnormal membrane association and dynamic behavior of progerin/LA-delta-50 during mitosis, which lead to aberrant chromosome segregation in both HGPS and normal cells. These observations further implicate progerin/LA-delta-50 in the normal aging process, suggesting that the same molecular mechanisms responsible for the mitotic defects in HGPS may also act at a low level in normal cells at higher passage. Taken together with results of previous studies, these data add increasing confidence to the long-held assumption that the study of genetic forms of premature aging can shed important light on the normal process of aging.”

    One of the co-authors of the paper is Francis S. Collins, head of the Human Genome Project. Dr. Collins is a church-going, born-again Christian whose recent book, The Language of God: A Scientist Presents Evidence for Belief, expounded his own theistic-evolution position on origins.
    --------------------------------------------------------------------------------
    1Cao, Capell, Erdos, Djabali, and Collins, “A lamin A protein isoform overexpressed in Hutchinson-Gilford progeria syndrome interferes with mitosis in progeria and normal cells,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0611640104, published online before print March 14, 2007.
    2“This mutation does not cause an amino acid change (G608G), but partially activates a cryptic splice donor site and leads to the in-frame deletion of 150 bp within the prelamin A mRNA. This truncated prelamin A mRNA is then translated into a protein recently named progerin/LA-delta-50. The Zmpste24/FACE1 cleavage site is missing in progerin/LA-delta-50 because of the internal 50-aa [amino acid] deletion, so that progerin/LA-delta-50 retains the C-terminal farnesylation.”
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

  14. #59
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    Another “Complex and Powerful Molecular Motor” 03/20/2007
    DNA is an extremely long molecule that is packed into a very small space by tiny machines in the cell dedicated to this task. After human cell division, the molecules are wound tightly into coils that are in turn wound into loops. These coils and loops make up a chromosome that we see under the microscope in the nucleus of a cell.
    In Bacillus subtilis bacteriophage Phi-29 the DNA molecule is packed after cell division into a hollow shell by a unique machine. The way that this machine works was the subject of investigation by a team of scientists. Competing theories had the machine either rotating the DNA strands as it packed them into the shell, or just pushing them in. Researchers attached tiny magnets to the ends of the DNA strands to stretch them out, and attached fluorescent tags onto the DNA strands to determine if the strands were being rotated. The results of the study found no rotation:

    “How, then, does it happen? The researchers noted that their findings are compatible with a recently proposed nonrotating model in which the ring of ATPases alternately compresses and extends, drawing the DNA in—a bit like what your mouth might do if you had to eat a plateful of spaghetti with your hands tied behind your back.”

    A description of the project is published online in Public Library of Science.1 The article begins, “You probably never tried to put toothpaste back into the tube, but if you did, you’d have a good idea of what the Bacillus subtilis bacteriophage phi-29 experiences as it crams its DNA into a protein capsid shell following replication.”

    1Hoff M (2007) Does Bacteriophage Phi-29 Pack Its DNA with a Twist? PLoS Biol 5(3): e91 Public Library of Science, published online: February 20, 2007; doi:10.1371/journal.pbio.0050091.

    Another amazing machine shows up in the cell just for the purpose of packing DNA. Rings of ATP alternately compress to push strands of DNA into a cellular storage container for safe keeping. The author describes the machine as “a complex and powerful molecular motor,” and truly it is. Perhaps evolutionists could explain how the cell managed before this complex machine accidentally appeared on the scene to deal with the great wad of DNA that must have been getting in the way of the operation of the cell. The author gives us no clue: evolution is not mentioned once in the article.
    -DK
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

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    I am bumping this thread to the top so that newcomers can get a feel (using mainline scientific journal articles) for what is going on within the cells of lifeforms.
    Random changes are destructive to any carefully crafted piece of work, such as a computer program, a novel or the genome of a lifeform.
    Matt 23:24Ye blind guides, which strain at a gnat, and swallow a camel.

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