Biomolecular machines

Just to highlight replication machinery and how it operates again:

How 'molecular machines' kick start gene activation revealed

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Activator protein is shown to start gene transcription process. (Credit: Image courtesy of Imperial College London)​

How 'molecular machines' inside cells swing into action to activate genes at different times in a cell's life is revealed today (6 November) in new research published in Molecular Cell. Genes are made of double stranded DNA molecules containing the coded information an organism's cells need to produce proteins. The DNA double strands need to be 'melted out' and separated in order for the code to be accessed. Once accessed, the genetic codes are converted to messenger RNAs (mRNA) which are used to make proteins. Cells need to produce particular proteins at different times in their lives, to help them respond and adapt to changes in their environment.
The "melting out" process is carried out by helicases which is part of the replisome. Exquisitely controlled.
Helicases are also known to be ring-shaped motor proteins, typically hexamers and separate double-stranded DNA into single-stranded templates for the replication machinery. Replication occurs at about 1000 base pairs per second due to the highly efficient combination of sliding clamps and the polymerases. Thus, helicases need to unwind DNA at at least that speed. Unwinding DNA too slowly and the replication machinery might break down . Unwind the DNA too fast or untimely and harmful mutations might occur as single-stranded DNA is prone to degradation and cytosine deamination. The speed at which helicase unwinds DNA is no accident though, as it is intrinsically controlled. As helicase is bound to the lagging strand, it unwinds the leading strand in a separate direction. Applying a pulling force on the leading strand leads to a 7-fold increase in the speed of DNA unwinding by helicase. The highly efficient DNA polymerase/sliding clamp combination provides this controlling force on the leading strand. This forms a robust unwinding/polymerization interaction whereby polymerization controls and prevents unwanted DNA unwinding.

The new study outlines exactly how a molecular machine called RNA polymerase, which reads the DNA code and synthesizes mRNA, is kickstarted by specialised activator proteins. The scientists have discovered that RNA polymerase uses a tightly regulated internal blocking system that prevents genes from being activated when they are not needed.

Using electron microscopy to look at the inner workings of bacterial cells, the researchers discovered that the DNA strand-separating process is kickstarted when RNA polymerase is modified by an activator protein, which the cell sends to the site of the gene that needs to be switched on.

This activator protein jump-starts the RNA polymerase machine by removing a plug which blocks the DNA's entrance to the machine. The activator protein also causes the DNA strands to shift position so that the DNA lines up with the entrance to the RNA polymerase. Once these two movements have occurred and the DNA strands are in position, the RNA polymerase machine gets to work melting them out, so that the information they contain can be processed to produce mRNA, and ultimately allow production of proteins.

Professor Xiaodong Zhang, lead author of the paper from the Department of Life Sciences at Imperial College London, explains the significance of the team's findings, saying:

"Understanding how the RNA polymerase gene transcription 'machine' is activated, and how it is stalled from working when it is not needed, gives us a better insight than ever before into the inner workings of cells, and the complex processes that occur to facilitate the carefully regulated production of proteins."

Professor Martin Buck, Head of Imperial's Division of Biology and one of the paper's co-authors, adds that understanding how this process works in bacteria cells is of particular interest, because it is this gene transcription and protein production process which allows bacterial cells to adapt, respond and thrive despite changes in their environment:

"In other words, this is the process that occurs inside bacteria that makes them so good at survival. Many bacteria cause infection and disease in humans, and are hard to defeat. Bacterial RNA polymerase is a proven target for antibiotics such as rifampicin, against which many bacteria have become resistant. Insights gained form our research will now provide opportunities and strategies for the design of novel antibacterial compounds," he concludes

Molecular machines govern the activity of gene expression.
Molecular machines are governed by gene expression through cell signaling that is governed by a reasonably optimal genetic code.
The genetic code is also very optimal for accepting new information yet the code is very stable.

Interesting not?
 
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Invitrogen has brought out a new product whereby you can introduce green fluorescent proteins (GFPs) into various cell lines via a simple viral vector. These GFPs can then be used for live cell imaging. They have some pretty amazing videos showing cells in real-time. Have fun:

Tubulin and actin

Histones
 
What is the cause of cellular repair and division? More machines....

Scientists Decipher Missing Piece Of First-responder DNA Repair Machine
ScienceDaily (Oct. 2, 2009) — Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory and the Scripps Research Institute have uncovered the role played by the least-understood part of a first-responder molecule that rushes in to bind and repair breaks in DNA strands, a process that helps people avoid cancer.

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The last piece of the MRN puzzle falls into place: Nbs1 molecules extend from the DNA repair machine like two flexible arms, as revealed by recent research at Berkeley Lab's Advanced Light Source. In this illustration, the MRN complex bridges a DNA double-strand break where the green and blue DNA sections meet.


With this final piece of the puzzle in place, scientists can better understand how the repair mechanism fends off cancer in healthy people, and conversely, how it helps cancer cells resist chemotherapy. This could enable researchers to develop more effective therapies with fewer side effects.

The team deciphered the poorly understood component using innovative x-ray imaging techniques at Berkeley Lab’s Advanced Light Source, which generates intense light for scientific research. They found that it extends from the repair machinery like a flexible arm and grabs molecules that are needed to help the machine zip severed DNA strands back together.

Their work is published in the October 2, 2009 issue of the journal Cell.

“This not only reveals how life works at a fundamental level, but also promises to guide the development of cancer treatments,” says John Tainer of Berkeley Lab’s Life Sciences Division and the Scripps Research Institute in La Jolla, CA. Tainer co-led the research with Paul Russell of the Scripps Research Institute.

The first-responder machine, a protein complex called Mre11-Rad50-Nbs1 (or MRN for short), homes in on the gravest kind of breaks in which both strands of a DNA double helix are cut. It then stops the cell from dividing and launches an error-free DNA repair process called homologous recombination, which replaces defective genes. If unrepaired, double strand breaks can lead to the proliferation of cancer cells.

Unfortunately, MRN’s laser-like focus on DNA repair means that it also mends broken DNA in cancerous cells. This sometimes stymies chemotherapy treatments that kill cancer cells by inducing double strand DNA breaks.

Because of its key roles — good and bad — scientists have painstakingly studied MRN since 1995 to learn how it works in healthy people, how its mutations promote diseases such as cancer, and to possibly disable it during cancer treatment.

Despite more than a decade of effort, a critical part was missing: a protein called Nbs1 that is represented by the ‘N’ in MRN.

To determine Nbs1’s function, the team used an Advanced Light Source beamline called SIBYLS, which yields extremely high-resolution images of the crystal structure of a protein via a technique called x-ray crystallography. The beamline is also equipped with small-angle x-ray scattering, which can determine a protein’s overall architecture in solution, a critical step that approximates how a protein appears in its natural state — such as inside a cell.

The scientists trained these two tools on human and yeast Nbs1 proteins. (DNA repair is so essential to life that many of the molecular machines that perform it have changed little throughout evolution). Importantly, the team studied Nbs1 bound to a partner protein that opens DNA during the first steps of double strand break repair. This enabled them to observe Nbs1 at work.

They found that Nbs1 attaches to the MR protein complex precisely where the protein complex converges on the DNA break. Nbs1 also bends in the middle like an elbow to channel molecules to the repair site.

These insights offer the best glimpse yet of how Nbs1 works and how damaged Nbs1 can lead to disease. It also suggests ways to monkey wrench MRN so that it can’t repair DNA during chemotherapy. Perhaps a molecule can be wedged into Nbs1’s elbow joint so it can’t bend, rendering the MRN complex useless.

“These crystal and solution structures have given us an exciting leap forward in our understanding of the Nbs1 and how defects in the protein cause disease,” says Scott Classen of Berkeley Lab’s Physical Biosciences Division.

Adds Tainer, “Understanding how the body responds to DNA breaks is fundamental for cancer interventions and gene therapies. These results open the door to controlling the repair of DNA breaks for cancer therapeutics and gene targeting.”

The research was funded by in part by grants from the National Cancer Institute of the National Institutes of Health. Berkeley Lab’s Advanced Light Source is supported by the U.S. Department of Energy’s Office of Science.

The SIBYLS beamline is supported by the U.S. Department of Energy’s Office of Science and the National Institutes of Health.
 
Telomere Copy Protection: Nobel Goes To Scientists Who Solved How Chromosome Ends Work
ScienceDaily (Oct. 5, 2009) — This year's Nobel Prize in Physiology or Medicine is awarded to three scientists who have solved a major problem in biology: how the chromosomes can be copied in a complete way during cell divisions and how they are protected against degradation. The Nobel Laureates have shown that the solution is to be found in the ends of the chromosomes – the telomeres – and in an enzyme that forms them – telomerase.

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Telomere illustration. (Credit: Copyright The Nobel Committee for Physiology or Medicine 2009 / Illustration: Annika Röhl)

The long, thread-like DNA molecules that carry our genes are packed into chromosomes, the telomeres being the caps on their ends. Elizabeth Blackburn and Jack Szostak discovered that a unique DNA sequence in the telomeres protects the chromosomes from degradation. Carol Greider and Elizabeth Blackburn identified telomerase, the enzyme that makes telomere DNA. These discoveries explained how the ends of the chromosomes are protected by the telomeres and that they are built by telomerase.

If the telomeres are shortened, cells age. Conversely, if telomerase activity is high, telomere length is maintained, and cellular senescence is delayed. This is the case in cancer cells, which can be considered to have eternal life. Certain inherited diseases, in contrast, are characterized by a defective telomerase, resulting in damaged cells. The award of the Nobel Prize recognizes the discovery of a fundamental mechanism in the cell, a discovery that has stimulated the development of new therapeutic strategies.

The mysterious telomere

The chromosomes contain our genome in their DNA molecules. As early as the 1930s, Hermann Muller (Nobel Prize 1946) and Barbara McClintock (Nobel Prize 1983) had observed that the structures at the ends of the chromosomes, the so-called telomeres, seemed to prevent the chromosomes from attaching to each other. They suspected that the telomeres could have a protective role, but how they operate remained an enigma.

When scientists began to understand how genes are copied, in the 1950s, another problem presented itself. When a cell is about to divide, the DNA molecules, which contain the four bases that form the genetic code, are copied, base by base, by DNA polymerase enzymes. However, for one of the two DNA strands, a problem exists in that the very end of the strand cannot be copied. Therefore, the chromosomes should be shortened every time a cell divides – but in fact that is not usually the case.

Both these problems were solved when this year's Nobel Laureates discovered how the telomere functions and found the enzyme that copies it.

Telomere DNA protects the chromosomes

In the early phase of her research career, Elizabeth Blackburn mapped DNA sequences. When studying the chromosomes of Tetrahymena, a unicellular ciliate organism, she identified a DNA sequence that was repeated several times at the ends of the chromosomes. The function of this sequence, CCCCAA, was unclear. At the same time, Jack Szostak had made the observation that a linear DNA molecule, a type of minichromosome, is rapidly degraded when introduced into yeast cells.

Blackburn presented her results at a conference in 1980. They caught Jack Szostak's interest and he and Blackburn decided to perform an experiment that would cross the boundaries between very distant species. From the DNA of Tetrahymena, Blackburn isolated the CCCCAA sequence. Szostak coupled it to the minichromosomes and put them back into yeast cells. The results, which were published in 1982, were striking – the telomere DNA sequence protected the minichromosomes from degradation. As telomere DNA from one organism, Tetrahymena, protected chromosomes in an entirely different one, yeast, this demonstrated the existence of a previously unrecognized fundamental mechanism. Later on, it became evident that telomere DNA with its characteristic sequence is present in most plants and animals, from amoeba to man.

An enzyme that builds telomeres


Carol Greider, then a graduate student, and her supervisor Blackburn started to investigate if the formation of telomere DNA could be due to an unknown enzyme. On Christmas Day, 1984, Greider discovered signs of enzymatic activity in a cell extract. Greider and Blackburn named the enzyme telomerase, purified it, and showed that it consists of RNA as well as protein. The RNA component turned out to contain the CCCCAA sequence. It serves as the template when the telomere is built, while the protein component is required for the construction work, i.e. the enzymatic activity. Telomerase extends telomere DNA, providing a platform that enables DNA polymerases to copy the entire length of the chromosome without missing the very end portion.

Telomeres delay aging of the cell

Scientists now began to investigate what roles the telomere might play in the cell. Szostak's group identified yeast cells with mutations that led to a gradual shortening of the telomeres. Such cells grew poorly and eventually stopped dividing. Blackburn and her co-workers made mutations in the RNA of the telomerase and observed similar effects in Tetrahymena. In both cases, this led to premature cellular aging – senescence. In contrast, functional telomeres instead prevent chromosomal damage and delay cellular senescence. Later on, Greider's group showed that the senescence of human cells is also delayed by telomerase. Research in this area has been intense and it is now known that the DNA sequence in the telomere attracts proteins that form a protective cap around the fragile ends of the DNA strands.

An important piece in the puzzle – human aging, cancer, and stem cells

These discoveries had a major impact within the scientific community. Many scientists speculated that telomere shortening could be the reason for aging, not only in the individual cells but also in the organism as a whole. But the aging process has turned out to be complex and it is now thought to depend on several different factors, the telomere being one of them. Research in this area remains intense.

Most normal cells do not divide frequently, therefore their chromosomes are not at risk of shortening and they do not require high telomerase activity. In contrast, cancer cells have the ability to divide infinitely and yet preserve their telomeres. How do they escape cellular senescence? One explanation became apparent with the finding that cancer cells often have increased telomerase activity. It was therefore proposed that cancer might be treated by eradicating telomerase. Several studies are underway in this area, including clinical trials evaluating vaccines directed against cells with elevated telomerase activity.

Some inherited diseases are now known to be caused by telomerase defects, including certain forms of congenital aplastic anemia, in which insufficient cell divisions in the stem cells of the bone marrow lead to severe anemia. Certain inherited diseases of the skin and the lungs are also caused by telomerase defects.

In conclusion, the discoveries by Blackburn, Greider and Szostak have added a new dimension to our understanding of the cell, shed light on disease mechanisms, and stimulated the development of potential new therapies.

Elizabeth H. Blackburn has US and Australian citizenship. She was born in 1948 in Hobart, Tasmania, Australia. After undergraduate studies at the University of Melbourne, she received her PhD in 1975 from the University of Cambridge, England, and was a postdoctoral researcher at Yale University, New Haven, USA. She was on the faculty at the University of California, Berkeley, and since 1990 has been professor of biology and physiology at the University of California, San Francisco.

Carol W. Greider is a US citizen and was born in 1961 in San Diego, California, USA. She studied at the University of California in Santa Barbara and in Berkeley, where she obtained her PhD in 1987 with Blackburn as her supervisor. After postdoctoral research at Cold Spring Harbor Laboratory, she was appointed professor in the department of molecular biology and genetics at Johns Hopkins University School of Medicine in Baltimore in 1997.

Jack W. Szostak is a US citizen. He was born in 1952 in London, UK and grew up in Canada. He studied at McGill University in Montreal and at Cornell University in Ithaca, New York, where he received his PhD in 1977. He has been at Harvard Medical School since 1979 and is currently professor of genetics at Massachusetts General Hospital in Boston. He is also affiliated with the Howard Hughes Medical Institute.

Ageing and telomerase seem to be linked, but so is cancer and telomerase. Many cancer cell lines are immotalized in part due to the uncontrolled expression of telomerase.

Anybody willing to be an immortal cancerous blob?
 
New and interesting information regarding nuclear pore machines:

'Promiscuous' Protein Interactions Found In The Nuclear Pore Complex

ScienceDaily (Oct. 3, 2009) — In higher organisms, cells are very selective about what passes in and out of their nuclei, where the genes reside. This selectivity helps protect the DNA and is the job of machines that stud the envelope of the nucleus, called nuclear pore complexes. These gatekeepers have proved largely inscrutable to researchers over the years, despite their conspicuously large size (they are made of 30 different proteins, or nucleoporins), but bit by bit, scientists are learning how these machines work.

Now a new study reveals the molecular structure of the largest piece of the molecule-trafficking complex to be captured by x-ray crystallography to date. Researchers have also shown that one member of the three-protein structure interacts promiscuously with two nucleoporins as do other proteins in the nuclear pore, supporting a model of a flexible complex that can rearrange itself into different formations. The work suggests an important design feature of this transport organelle, an ancient evolutionary innovation fundamental to the development of multicellular life on Earth.

The research, performed by Vivien Nagy, a visiting graduate student, André Hoelz, a research associate, and colleagues in Rockefeller University’s Laboratory of Cell Biology, uncovered the molecular structure of three interacting proteins that form the centerpiece of the Nup84 complex — an important structural component of the nuclear pore complex. The Nup84 complex is a Y-shaped heptamer — a molecule composed of seven units — that was recently imaged in three dimensions by Martin Kampmann, also a member of the lab headed by Günter Blobel, John D. Rockefeller Jr. Professor and an investigator at the Howard Hughes Medical Institute. In experiments to be published online in the Proceedings of the National Academy of Sciences, in September Nagy, Hoelz and colleagues provide the molecular specifics of the only piece of the Nup84 complex that remained unknown, furthering the structural characterization of this building module. They also describe competing interactions within the Nup84 complex and discuss the possibility of binding promiscuity as a common feature in the nuclear pore complex. These findings suggest that more than one assemblage of its elements may be necessary for the function of the nuclear pore complex — to import and export macromolecules including ribosomes and messenger RNA.

“Now that we realize that promiscuity may be a major factor in the nuclear pore complex — that the nucleoporins have different ways of interacting with each other — the complex is no longer just a three-dimensional jigsaw puzzle,” Hoelz says. “Now we have to place these structures into a fourth dimension and find out when they adopt these different shapes. We’re trying to take snapshots, static pictures, and turn them into a movie. It will require a lot more pictures, a lot more structures, before we understand the function and dynamics of this intricate transport organelle.

Other related articles:
Molecular Machine Turns Packaged Messenger RNA Into A Linear Transcript
New Research Supports Model For Nuclear Pore Complex
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Paring the pore. A new model of how the nuclear pore complex might work suggests that an interaction between two proteins -- key elements of the yellow ring pictured above -- link together, forming a flexible fence around the pore's opening. (Credit: Joseph Alexander, Erik Debler and Andre Hoelz)

More information about nuclear pores:
[ame="http://www.youtube.com/watch?v=dJLeLRXIOj0"]Video[/ame]
[ame]http://www.youtube.com/watch?v=oYhN57EZx9Y&feature=related[/ame]

NuclearPore.jpg

nuclear_pore.png

nuclear_pore_complex.jpg
 
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Humble man this Prof Olovnikov :). Good on him, get on with the work and let the shena****ns carry on.
It seems to be a competitive rather than sharing game science. Even Crick allegedly 'stole' the idea of the DNA molecule from a British woman.
 
It seems to be a competitive rather than sharing game science. Even Crick allegedly 'stole' the idea of the DNA molecule from a British woman.
Publish or perish is a popular saying. If you don't publish, you don't get grants. Guess it depends on how bad you want to do research.

Seems Nobel prizes for figuring out how cells operate is popular this year:

Nobel Prize In Chemistry: What Ribosomes Look Like And How They Functions At Atomic Level

The ribosome in action.

[ame]http://www.youtube.com/watch?v=fN6S0C2RXYY[/ame]
 
3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell
ScienceDaily (Oct. 8, 2009) — Scientists have deciphered the three-dimensional structure of the human genome, paving the way for new insights into genomic function and expanding our understanding of how cellular DNA folds at scales that dwarf the double helix.

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Researchers have found that the genome adopts a "fractal globule" organization, enabling the cell to pack DNA incredibly tightly while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. (Credit: Image by Bang Wong, Broad Institute)

In a paper featured this week on the cover of the journal Science, they describe a new technology called Hi-C and apply it to answer the thorny question of how each of our cells stows some three billion base pairs of DNA while maintaining access to functionally crucial segments. The paper comes from a team led by scientists at Harvard University, the Broad Institute of Harvard and MIT, University of Massachusetts Medical School, and the Massachusetts Institute of Technology.

"We've long known that on a small scale, DNA is a double helix," says co-first author Erez Lieberman-Aiden, a graduate student in the Harvard-MIT Division of Health Science and Technology and a researcher at Harvard's School of Engineering and Applied Sciences and in the laboratory of Eric Lander at the Broad Institute. "But if the double helix didn't fold further, the genome in each cell would be two meters long. Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter. This new approach enabled us to probe exactly that question."

The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment. Chromosomes snake in and out of the two compartments repeatedly as their DNA alternates between active, gene-rich and inactive, gene-poor stretches.

"Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them," says Job Dekker, associate professor of biochemistry and molecular pharmacology at UMass Medical School and a senior author of the Science paper.

Second, at a finer scale, the genome adopts an unusual organization known in mathematics as a "fractal." The specific architecture the scientists found, called a "fractal globule," enables the cell to pack DNA incredibly tightly -- the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

"Nature's devised a stunningly elegant solution to storing information -- a super-dense, knot-free structure," says senior author Eric Lander, director of the Broad Institute, who is also professor of biology at MIT, and professor of systems biology at Harvard Medical School.

In the past, many scientists had thought that DNA was compressed into a different architecture called an "equilibrium globule," a configuration that is problematic because it can become densely knotted. The fractal globule architecture, while proposed as a theoretical possibility more than 20 years ago, has never previously been observed.

Key to the current work was the development of the new Hi-C technique, which permits genome-wide analysis of the proximity of individual genes. The scientists first used formaldehyde to link together DNA strands that are nearby in the cell's nucleus. They then determined the identity of the neighboring segments by shredding the DNA into many tiny pieces, attaching the linked DNA into small loops, and performing massively parallel DNA sequencing.

"By breaking the genome into millions of pieces, we created a spatial map showing how close different parts are to one another," says co-first author Nynke van Berkum, a postdoctoral researcher at UMass Medical School in Dekker's laboratory. "We made a fantastic three-dimensional jigsaw puzzle and then, with a computer, solved the puzzle."

Lieberman-Aiden, van Berkum, Lander, and Dekker's co-authors are Bryan R. Lajoie of UMMS; Louise Williams, Ido Amit, and Andreas Gnirke of the Broad Institute; Maxim Imakaev and Leonid A. Mirny of MIT; Tobias Ragoczy, Agnes Telling, and Mark Groudine of the Fred Hutchison Cancer Research Center and the University of Washington; Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, M.A. Bender, and John Stamatoyannopoulos of the University of Washington; and Bradley Bernstein of the Broad Institute and Harvard Medical School.

This work was supported by the Fannie and John Hertz Foundation, the U.S. Department of Defense, the National Science Foundation, the National Space Biomedical Research Institute, the National Human Genome Research Institute, the American Society of Hematology, the National Heart, Lung, and Blood Institute, the National Institute of Diabetes and Digestive and Kidney Diseases, the Keck Foundation, and the National Institutes of Health.
Stunningly elegant indeed.
 
Educational video about the calcium pump machine:

[ame="http://www.youtube.com/watch?v=Hni5QyiTjIs"]A Molecular Machine at Work: The Case of the Calcium Pump Protein [/ame]

Nearly 100% efficient use of energy
Specific for calcium ions
 
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More fascinating findings related to ribosomes.
Scientists Visualize Assembly Line Gears In Ribosomes, Cell's Protein Factory

ScienceDaily (Oct. 15, 2009) — Even as research on the ribosome, one of the cell's most basic machines, is recognized with a Nobel Prize, scientists continue to achieve new insights on the way ribosomes work.

Ribosomes are factories inside cells where messages coming from genes are decoded and new proteins pieced together on an assembly line. For the first time, scientists have a detailed picture of the ribosome trapped together with elongation factor G (EF-G), one of the enzymes that nudges the assembly line to move forward.

The results are published in the Oct. 16 issue of Science.

A team led by Venki Ramakrishnan at the MRC Laboratory of Molecular Biology in Cambridge, England analyzed crystals of the ribosome bound to EF-G using X-rays, and used the X-ray data to determine the molecular structure.

One member of the team, Christine Dunham, PhD, recently joined Emory University School of Medicine's Department of Biochemistry as an assistant professor.

The scientists obtained crystals by growing heat-tolerant bacteria found at thermal vents at the bottom of the ocean. They purified the ribosomes from the bacteria and then added polymers carefully selected to coax the ribosomes into lining up and forming crystals. In addition, they included an antibiotic – fusidic acid – which traps EF-G on the ribosome.

Previous efforts to crystallize ribosomes together with EF-G led to EF-G being displaced from the crystals. Dunham says the team was able to visualize the ribosome bound to EF-G only by shaving off part of the ribosome. Modifying the bacterial gene that encoded a part of the ribosome with a "very strange and elongated protein shape" allowed crystals that included EF-G to form.

Dunham says details from the new structure show that EF-G interacts closely with parts of the ribosome, suggesting how it moves the assembly line forward without slipping out of frame. In addition, it paves the way for studying interactions between the ribosome and other proteins similar to EF-G that fit into the same spot.

In her own research, Dunham is examining how viruses such as HIV, upon hijacking ribosomes, use special tricks that cause the assembly line to slip, as well as how other antibiotics and toxin proteins interact with parts of the ribosome.

The research was supported by the UK Medical Research Council, the Wellcome Trust, the Agouron Institute and the Louis-Jeantet Foundation.
 
More talk about cellular communication....
Milestone Discovery In Cell Behaviors

ScienceDaily (Oct. 18, 2009) — A team of international molecular scientists, led by a Monash University researcher has discovered a new, fast mechanism by which cells communicate change – for example their location during spreading of a cancer in the human body – to adjacent cells.

The discovery sheds new light on cell behaviour and could lead to the development on new drugs to combat diseases such as cancer, rheumatoid arthritis and Alzheimer's disease.

The team led by Monash University Associate Professor Martin Lackmann found that for one particular communicator between cells, an enzyme known as A-Disintegrin-And-Metalloprotease 10 (ADAM10), a change in the shape of its contender (communication partner) will start the communication process.

Scientists are interested in ADAM10 -- and the proteins that are split by this protease -- because it is critical in cellular mechanisms that underlie several major diseases.

"This communication process between cells forms the basis for the way in which certain diseases progress. This discovery will change how we understand cell behaviour and change how we consider the design of therapeutic drugs in this area" Associate Professor Lackmann said.

"This new concept in understanding of how cells communicate identifies a process that is much simpler than previously thought and which will profoundly impact the direction of future biomedical research in this area," he said.

"The research team found that instead of using complex signalling pathways, this communication system is really very direct and simple. In this case it is a transient switch in the overall shape of the contending cell surface receptor itself which activates the ADAM10 protease to communicate this change and its functional consequences to a neighbouring cell.

"The discovery of this switch opens new avenues for the development of drugs that recognise this changed shape and prevent the signalling to other cells, thus slowing or even halting the spread of disease.

The discovery was made using fluorescence and electron microscopy techniques, which allowed the observation of intact cells at single molecule resolution the changes in the shape of the cell surface receptor that occur during cell-to-cell communication.

The discovery was published online in the open-access journal PLoS Biology.

Live cell imaging from Invitrogen
[ame]http://www.youtube.com/watch?v=DA8DvDE_nZo[/ame]
 
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Vesicle transport and the myosin motorprotein: Along actin filaments and not microtubulin filaments.
[ame]http://www.youtube.com/watch?v=7sRZy9PgPvg[/ame]
 
in my humble limited opinion with fascination, I skim through the posts occassionally and check some of the links as it is leaves me in awe, dumb-founded and with renewed respect at the engineering complexities with perfection and precision.
Studying it authenticates The Author.
Looking for clues to validate anything else is taking snippets here and there and editing the much much bigger picture. However, the real question is "why?".
Why would one defend a theory that requires so much proof that is missing when there is so much evidence of devine engineering with life that reproduces nogal?
 
actually I wish I had the time to take it all in, the thread is a university course on it's own. Perhaps it should be published in lieu of all the other fictional text books trying to justify the trillions of years needed to turn the frog into a prince
 
Why would one defend a theory that requires so much proof that is missing when there is so much evidence of devine engineering with life that reproduces nogal?

So much proof that it's probably a better supported theory than gravity is...
 
Interesting article:
Probing Biomolecular Machines with Graphics Processors

The evolution of GPU processors and programming tools is making advanced simulation and analysis techniques accessible to a growing community of biomedical scientists.
The evolution of GPU processors is of course because of intelligent design :p.

This article is based on our experiences developing software for use by and in cooperation with scientists, often graduate students, with backgrounds in physics, chemistry, and biology. Our programs, NAMD18 (Nanoscale Molecular Dynamics) and VMD10 (Visual Molecular Dynamics), run on computer systems ranging from laptops to supercomputers and are used to model proteins, nucleic acids, and lipids at the atomic level in order to understand how protein structure enables cellular functions such as catalyzing reactions, harvesting sunlight, generating forces, and sculpting membranes (see http://www.ks.uiuc.edu/ for additional scientific applications). In 2007 we began working with the Nvidia CUDA (Compute Unified Device Architecture) system for general-purpose graphics processor programming to bring the power of many-core computing to practical scientific applications.22

NAMD and VMD are freely avaliable for moleular simulations (google "VMD"). And for those with a lot of extra CPU and GPU power and time can use already solved protein structures to model molecular machines and see how it works.

BOTTOM-UP BIOLOGY
If one were to design a system to safeguard critical data for thousands of years, it would require massive redundancy, self-replication, easily replaceable components, and easily interpreted formats. These are the same challenges faced by our genes, which build around themselves cells, organisms, populations, and entire species for the sole purpose of continuing their own survival. The DNA of every cell contains both data (the amino acid sequences of every protein required for life) and metadata (large stretches of “junk” DNA that interact with hormones to control if a sequence is exposed to the cell’s protein expression machinery or hidden deep inside the coils of the chromosome).
Interesting, if you want to design something that last for thousands, even millions of years, you will need the following:
1) massive redundancy
2) self-replication
3) easily replaceable components
4) easily interpreted formats

Let's see what we have in all organisms:
1) massive redundancy?
Well yes, lots of it, as well as resiliency:
Cells Are Like Robust Computational Systems, Scientists Report
Computational Biology Illuminates How Cells Change Gears
2) self-replication?
Of course
3) easily replaceable components?
Cells make their own components, have been doing it for millions of years.
4) easily interpreted formats
Well, the genetic code has been around since the start of life as we know it. It is one of the least evolvable elements of life and it is very optimal for incorporating new information. The nature of the code (e.g. cytosine deamination) also plays a pivotal role in immune function and "looking after itself" through the functions of p53 (guardian of the genome).

Good to know all the elements needed for something to last as long as life did were present from the onset :). Including a little "junk" in the trunk just to let things go a little smoother :D.

The article continues with lots of interesting information regarding future ideas for biomolecular machine simulations, GPU programming etc. Have fun.
 
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Good to know all the elements needed for something to last as long as life did were present from the onset :). Including a little "junk" in the trunk just let things go a little smoother :D.

Really enjoy your commentary on the fascinating topics...
:p getting a free education here as well!

Just added science daily to my favourites

Admire your stance too.
 
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