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  • richardmitnick 11:20 am on December 4, 2016 Permalink | Reply
    Tags: , , Cell studies, ,   

    From Weizmann: “When Cells Are Fit” 

    Weizmann Institute of Science logo

    Weizmann Institute of Science

    07.11.2016 [I guess this has just ben in hiding.]
    No writer credit found

    How do the expression levels of numerous proteins affect a cell’s fitness?

    Tracking protein activity levels in a cell is essential to the study of such diseases as cancer which, alongside changes in the genes, involves changes in the activity levels of numerous proteins. However, deducing function, fitness and cellular well-being from the growing number of protein level measurements is still a major challenge. For example, is a two-fold – or 100-fold – range in activity for a particular protein tolerable over the population, or does it herald differences in the way that the cells carry out their tasks? Charting this connection could transform the way we diagnose, monitor and treat patients.

    (l-r) Maya Lotan-Pompan, Leeat Yankielowicz Keren and Prof. Eran Segal can now look at multiple protein expression levels at once

    “Most experiments examining ranging protein activity levels have, until now, focused on single proteins. What we did was to develop a way to systematically vary activity levels for hundreds of different proteins – all in a single experiment – and accurately measure how this affects the function of the cells,” says Leeat Yankielowicz Keren, a research student in the group of Prof. Eran Segal of the Computer Science and Applied Mathematics, and Molecular Cell Biology Departments at the Weizmann Institute of Science.

    The basic idea of the experiment in Segal’s lab was to create a competition in which common bakers’ yeast cells are pitted against one another. Each cell was nearly identical to its neighbors, except for a tweak to the activity level of one of its proteins. Thousands of these genetically engineered yeast cells were grown together in lab dishes; the “winners” were those in which expression levels boosted their fitness, basically enabling the yeast to eat more, grow and divide faster.

    Segal and his group developed a high-throughput genetic engineering technique that enabled them to manipulate the activity levels of different protein levels within thousands of cells simultaneously, precisely controlling, for each, the amounts of one particular protein. With 130 different activity levels – the highest 500 times the lowest – attached to 81 different protein-encoding sequences, the researchers created something like 10,000 different variations on the basic yeast cell, assigning each a “barcode” for convenient identification. With a combination of DNA sequencing techniques and an algorithm they created to reconstruct the growth rates of the various yeast cells, the team was then able to accurately map the connections between protein levels and the fitness of the cell.

    The competition took place in two different “arenas.” In one, the yeast were fed the glucose sugar they prefer; in the second, they were fed a different kind of sugar, galactose. The team found that when the competition took place on the kind of sugar it prefers, the original, untouched version of the yeast cell was the overall winner – testimony to the efficiency of evolution. But on the second kind of sugar, others came out on top. These results showed that around 20% of the yeast’s natural protein activity levels are too low or too high for growing on this sugar. This could be relevant to biotechnology: The second sugar is cheaply and abundantly found in seaweed, and the yeast break it down into ethanol, which can be burned in place of fossil fuels. The study suggests that genetically engineering yeast to alter some of these protein levels could significantly increase the efficiency of this process.

    Mapping all the activity patterns together enabled the group to begin to see patterns in the chaos. Similar activity patterns, for example, pointed to proteins that work together. Further analysis even revealed the “math” that cells use to produce these proteins in the right ratios, for example, for the construction of complexes that require exact proportions of their various proteins.

    Some of the proteins appeared to operate in a very narrow range – levels even a bit below or above this range drastically affected the fitness of the yeast. Others seemed to be much more flexible – a little or a lot did not affect the cell’s fitness, at least for the particular growing conditions. Those showing the larger ranges in the fitness competition turned out to be proteins that ordinarily vary widely from cell to cell in the natural yeast population. These findings suggest that understanding this flexibility can shed light on how activity levels are selected in evolution.

    Gene fitness profiles are different when yeast are grown on a sugar they normally prefer less

    For Segal and his team, the future goal is to create similar maps for protein activity levels in human cells. Such maps could form the basis of future diagnostic techniques that would be much more refined and precise than those of today, based on blood tests that already exist or can easily be developed. They might reveal the effects of diet or medications; and they could provide early diagnosis of cancer. Keren: “We want to eventually create a ‘chart’ that doctors can use to know which protein levels to check, and what levels should, ideally, be appearing in order to prevent disease.”

    Also participating in this study were Maya Lotan-Pompan and Dr. Adina Weinberger of Prof. Segal’s group, Dr. Jean Hausser and Prof. Uri Alon of the department of Molecular Cell Biology and Prof. Ron Milo of the department of Plant and Environmental Sciences.

    Science paper:
    Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness, Cell

    See the full article here .

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    Weizmann Institute Campus

    The Weizmann Institute of Science is one of the world’s leading multidisciplinary research institutions. Hundreds of scientists, laboratory technicians and research students working on its lushly landscaped campus embark daily on fascinating journeys into the unknown, seeking to improve our understanding of nature and our place within it.

    Guiding these scientists is the spirit of inquiry so characteristic of the human race. It is this spirit that propelled humans upward along the evolutionary ladder, helping them reach their utmost heights. It prompted humankind to pursue agriculture, learn to build lodgings, invent writing, harness electricity to power emerging technologies, observe distant galaxies, design drugs to combat various diseases, develop new materials and decipher the genetic code embedded in all the plants and animals on Earth.

    The quest to maintain this increasing momentum compels Weizmann Institute scientists to seek out places that have not yet been reached by the human mind. What awaits us in these places? No one has the answer to this question. But one thing is certain – the journey fired by curiosity will lead onward to a better future.

  • richardmitnick 7:11 am on September 6, 2016 Permalink | Reply
    Tags: , , Cell studies,   

    From Max Planck Gesellschaft: “Hungry cells on the move” 

    MPG bloc

    Max Planck Gesellschaft

    September 06, 2016
    rof. Dr. Rüdiger Klein
    Max Planck Institute of Neurobiology, Martinsried
    Phone:+49 89 8578-3151Fax:+49 89 8578-3152

    Dr. Stefanie Merker
    Max Planck Institute of Neurobiology, Martinsried
    Phone:+49 89 8578-3514

    Researchers discover a signalling pathway that enables cells to reach their destinations through repulsion

    When cells grow and divide, they come into contact with other cells. This happens not only during development and regeneration and after injury, but also during cancer growth and the formation of metastases. When cells come into contact with each other in this way, information is exchanged by proteins, which are embedded in the cell membranes and form tight lock-and-key complexes with each other. These connections must be severed if the cells want to transmit a repulsion signal. It appears that the fastest way to do this is for the cells to engulf the protein complex from the membrane of the neighbouring cell. Scientists from the Max Planck Institute of Neurobiology in Martinsried have now identified the molecules that control this process.

    Ephrins (blue) and Ephs (red) form complexes (yellow) at cell contact points. To enable the cells to separate from each other, they are pulled into one of the cells with the help of the signalling proteins Tiam and Rac.
    © MPI of Neurobiology/Gaitanos

    Development is an extremely rapid process. Increasing numbers of cells are formed which must find their correct position in the body, clearly demarcate themselves from each other to form tissue, or – as is the case in the nervous system – establish contact with partner cells in remote locations. “The crowding is accompanied by orderly pushing and shoving,” says Rüdiger Klein, whose Department at the Max Planck Institute of Neurobiology studies how cells get their bearings. “A popular way for one cell to show another which direction to take is for it to repel the other cell following brief contact.” According to the scientists’ observations, the cells do not exactly treat each other with kid gloves and even go so far as to engulf entire pieces from the membranes of other cells.

    When cells come into contact with each other, ephrin and Eph receptors are often involved. These proteins are located on the surface of almost all cells. When two cells meet, their ephrin and Eph receptors connect to form tight ephrin/Eph complexes. These complexes then trigger the repulsion process through intracellular signalling pathways. “This is where the problem arises, as it appears that the cells then want to separate as quickly as possible – however, the two cells are attached to each other through the tight ephrin/Eph complex,” explains Klein. So the cells do something else: they extend their own cell membranes so far over the individual complexes that the complex and the surrounding membrane detaches from the neighbouring cell and is fully incorporated into the cell.
    Left: Ephrin and Eph receptors are found on the surface of almost all cells. Centre: When cells come into contact with each other, the two proteins form a tight complex. This triggers a signalling chain which causes the cell membrane to protrude. This process is controlled by the Tiam and Rac molecules and results in the reformation of the actin cytoskeleton. Right: The cells separate when one cell fully engulfs the ephrin/Eph complex through endocytosis.

    Left: Ephrin and Eph receptors are found on the surface of almost all cells. Centre: When cells come into contact with each other, the two proteins form a tight complex. This triggers a signalling chain which causes the cell membrane to protrude. This process is controlled by the Tiam and Rac molecules and results in the reformation of the actin cytoskeleton. Right: The cells separate when one cell fully engulfs the ephrin/Eph complex through endocytosis.

    The Max Planck researchers discovered as early as 2003 that cells can use this process, known as endocytosis, to separate from each other. Thanks to progress made in molecular biology since then, they have now managed to show how the process is controlled in detail.

    With the help of a series of genetic modifications and the targeted deactivation of individual cell components, the scientists succeeded in demonstrating that Tiam signalling proteins are activated through the formation of the ephrin/Eph complex. As a result, Rac enzymes become active which, in turn, cause the engulfment of the ephrin/Eph complexes by the cell membrane through the local restructuring of the actin cytoskeleton. If one of these components is missing, this engulfing process through endocytosis is blocked and the cells do not repel each other but remain attached.

    The clarification of this signalling pathway is important, as it provides a better understanding of the development of neuronal networks and other organ systems. The findings are also of considerable interest for cancer research: thanks to their ability to control cell repulsion, ephrin and Eph receptors play a major role in the penetration of tissue by cancer cells and in the formation of metastases. For this reason, receptors and their connection partners are the focus of current medical research. Better understanding of this signalling pathway, through which cell repulsion is controlled, could enable the development of new drugs to combat cancer.

    Original publication:
    Thomas N. Gaitanos, Jorg Koerner, Rüdiger Klein
    Tiam/Rac signaling mediates trans-endocytosis of ephrin receptor EphB2 and is important for cell repulsion.
    Journal of Cell Biology; 5 September, 2016

    See the full article here .

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    MPG campus

    The Max Planck Society for the Advancement of Science (German: Max-Planck-Gesellschaft zur Förderung der Wissenschaften e. V.; abbreviated MPG) is a formally independent non-governmental and non-profit association of German research institutes founded in 1911 as the Kaiser Wilhelm Society and renamed the Max Planck Society in 1948 in honor of its former president, theoretical physicist Max Planck. The society is funded by the federal and state governments of Germany as well as other sources.

    According to its primary goal, the Max Planck Society supports fundamental research in the natural, life and social sciences, the arts and humanities in its 83 (as of January 2014)[2] Max Planck Institutes. The society has a total staff of approximately 17,000 permanent employees, including 5,470 scientists, plus around 4,600 non-tenured scientists and guests. Society budget for 2015 was about €1.7 billion.

    The Max Planck Institutes focus on excellence in research. The Max Planck Society has a world-leading reputation as a science and technology research organization, with 33 Nobel Prizes awarded to their scientists, and is generally regarded as the foremost basic research organization in Europe and the world. In 2013, the Nature Publishing Index placed the Max Planck institutes fifth worldwide in terms of research published in Nature journals (after Harvard, MIT, Stanford and the US NIH). In terms of total research volume (unweighted by citations or impact), the Max Planck Society is only outranked by the Chinese Academy of Sciences, the Russian Academy of Sciences and Harvard University. The Thomson Reuters-Science Watch website placed the Max Planck Society as the second leading research organization worldwide following Harvard University, in terms of the impact of the produced research over science fields.

  • richardmitnick 11:14 am on June 7, 2016 Permalink | Reply
    Tags: , , Cell studies, Lund University   

    From AAAS: “Genetic code of red blood cells discovered” 



    Johan FlygareMD, PhD
    Assistant Professor, Lund University, Sweden
    Tel: +46 727 395959
    E-mail: johan.flygare@med.lu.se

    Johan Flygare and Sandra Capellera. Credit: Photo: Åsa Hansdotter / Lund University

    Eight days. That’s how long it takes for skin cells to reprogram into red blood cells. Researchers at Lund University in Sweden, together with colleagues at Center of Regenerative Medicine in Barcelona, have successfully identified the four genetic keys that unlock the genetic code of skin cells and reprogram them to start producing red blood cells instead.

    “We have performed this experiment on mice, and the preliminary results indicate that it is also possible to reprogram skin cells from humans into red blood cells. One possible application for this technique is to make personalised red blood cells for blood transfusions, but this is still far from becoming a clinical reality”, says Johan Flygare, manager of the research group and in charge of the study.

    Every individual has a unique genetic code, which is a complete instruction manual describing exactly how all the cells in the body are formed. This instruction manual is stored in the form of a specific DNA sequence in the cell nucleus. All human cells — brain, muscle, fat, bone and skin cells — have the exact same code. The thing that distinguishes the cells is which chapter of the manual the cells are able to read. The research group in Lund wanted to find out how the cells open the chapter that contains instructions on how to produce red blood cells. The skin cells on which the study was based had access to the instruction manual, but how were the researchers able to get them to open the chapter describing red blood cells?

    With the help of a retrovirus, they introduced different combinations of over 60 genes into the skin cells’ genome, until one day they had successfully converted the skin cells into red blood cells. The study is published in the scientific journal Cell Reports.

    “This is the first time anyone has ever succeeded in transforming skin cells into red blood cells, which is incredibly exciting”, says Sandra Capellera, doctoral student and lead author of the study.

    The study shows that out of 20,000 genes, only four are necessary to reprogram skin cells to start producing red blood cells. Also, all four are necessary in order for it to work.

    “It’s a bit like a treasure chest where you have to turn four separate keys simultaneously in order for the chest to open”, explains Sandra.

    The discovery is significant from several aspects. Partly from a biological point of view — understanding how red blood cells are produced and which genetic instructions they require – but also from a therapeutic point of view, as it creates an opportunity to produce red blood cells from the skin cells of a patient. There is currently a lack of blood donors for, for instance, patients with anaemic diseases. Johan Flygare explains:

    “An ageing population means more blood transfusions in the future. There will also be an increasing amount of people coming from other countries with rare blood types, which means that we will not always have blood to offer them”.

    Red blood cells are the most common cells in the human body, and are necessary in order to transport oxygen and carbon dioxide. Millions of people worldwide suffer from anaemia — a condition in which the patient has an insufficient amount of red blood cells. Patients with chronic anaemia are among the most problematic cases. They receive regular blood transfusions from different donors, which can eventually lead to the patient developing a reaction to the new blood. They simply become allergic to the donor’s blood. Finding a feasible way to make blood from an individual’s own skin cells would bring relief to this group of patients. However, further studies on how the generated blood performs in living organisms are needed.

    Defining the Minimal Factors Required for Erythropoiesis through Direct Lineage Conversion. Published in Cell Reports on June 2, 2016

    See the full article here .

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

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  • richardmitnick 2:26 pm on May 13, 2016 Permalink | Reply
    Tags: , , Cell studies, Look, Ma! No Mitochondria, ,   

    From NPR: “Look, Ma! No Mitochondria” 


    National Public Radio (NPR)

    May 12, 2016
    Nell Greenfield Boyce
    These mitochondria, in red, are from the heart muscle cell of a rat. Mitochondria have been described as “the powerhouses of the cell” because they generate most of a cell’s supply of chemical energy. But at least one type of complex cell doesn’t need ’em, it turns out.
    Science Source

    Scientists have found a microbe that does something textbooks say is impossible: It’s a complex cell that survives without mitochondria.

    Mitochondria are the powerhouses inside eukaryotic cells, the type of complicated cell that makes up people, other critters and plants and fungi. All eukaryotic cells contain a nucleus and little organelles — and one of the most famous was the mitochondrion.

    “They were considered to be absolutely indispensable components of the eukaryotic cell and the hallmark of the eukaryotic cell,” says Anna Karnkowska, a researcher in evolutionary biology at the University of British Columbia in Vancouver. Karnkowska and her colleagues describe their new find in a study published* online Thursday in the journal Current Biology.

    This is a light micrograph of the microbe that evolutionary biologists say lives just fine without any mitochondria.
    Naoji Yubuki/Current Biology

    Mitochondria have their own DNA, and scientists believe they were once free-living bacteria that got engulfed by primitive, ancient cells that were evolving to become the complex life forms we know and love today.

    For decades, researchers have tried to find eukaryotic cells that don’t have mitochondria — and for a while they thought they’d found some. One example is Giardia, a human gut parasite that causes diarrhea. It was considered to be a kind of living fossil because it had a nucleus but didn’t seem to have acquired mitochondria. But additional studies on Giardia and other microbes showed that actually, the mitochondria were there.

    “It turned out that all of them actually had some kind of remnant mitochondrion,” says Karnkowska, who notes that mitochondria perform key jobs in the cell beyond just generating power.

    A biggie is assembling iron-sulfur clusters for certain proteins, which is thought to be a mitochondrial function that’s really essential. So even if a microbe powers itself in a different way and has a limited form of the organelle that isn’t the same as the mitochondria found in people, Karnkowska says, “it’s still a mitochondrion and it has some important function for the cell.”

    That kind of vestigial mitochondrion is what she expected to find when she was a researcher at Charles University in Prague and started investigating a particular gut microbe that had been isolated from a researcher’s pet chinchilla.

    After she and her colleagues sequenced the gut microbe’s genome, however, they found no trace that it made any mitochondrial proteins at all. “So that’s a great surprise for us,” she says. “That should theoretically kill the cell — it shouldn’t exist.”

    What they learned is that instead of relying on mitochondria to assemble iron-sulfur clusters, these cells use a different kind of machinery. And it looks like they acquired it from bacteria.

    The researchers say this is the first example of any eukaryote that completely lacks mitochondria.

    Michael Gray, a biochemist at Dalhousie University in Halifax, Nova Scotia, says the researchers have made a “compelling” case that they have a bona fide eukaryote without any vestige of a mitochondrion; he calls the finding “unprecedented.”

    “The observation is significant, in that it clearly demonstrates that a eukaryote can still be a eukaryote without having a mitochondrion,” he tells Shots via email.

    However, the results do not negate the idea that the acquisition of a mitochondrion was an important and perhaps defining event in the evolution of eukaryotic cells, he adds.

    That’s because it seems clear that this organism’s ancestors had mitochondria that were then lost after the cells acquired their non-mitochondrial system for making iron-sulfur clusters.

    “This is not the missing link of eukaryotic evolution,” agrees Mark Van Der Giezen, a researcher in evolutionary biochemistry at the University of Exeter in the United Kingdom.

    Still, he says, it is an example of how flexible life is.

    “It lives in an area without oxygen and therefore can get rid of a lot of biochemistry that you and I would need in our cells to survive,” says Van Der Giezen. “This organism managed to adapt in such a way that it could lose an organelle, which every textbook will tell you is an essential feature of eukaryotes. That’s pretty amazing. It shows you that life is extremely creative in finding a way to eke out an existence.”

    *Science paper:
    A Eukaryote without a Mitochondrial Organelle

    See the full article here.

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  • richardmitnick 12:24 pm on April 15, 2016 Permalink | Reply
    Tags: , Cell studies,   

    From EMBL: “Revealing structure of nuclear pore’s inner ring” 

    EMBL European Molecular Biology Laboratory bloc

    European Molecular Biology Laboratory

    14 April 2016
    Sonia Furtado Neves, Science

    The architecture of the nuclear pore. The outer ring is colored in orange and blue, whereas the newly characterized inner ring is seen in green and lemon. Credit: Jan Kosinski/EMBL

    Study published today in Science sheds light on structure of nuclear pore complex, which plays a crucial role in controlling molecular traffic to a cell’s nucleus

    It was a 3D puzzle with over 1000 pieces, with only a rather fuzzy outline as a guide. But scientists at EMBL have now put enough pieces in place to see the big picture. In a study* published today in Science, they present their latest findings, bringing the nuclear pore complex into focus.

    The nuclear pore is a passage into the cell’s nucleus. A typical cell has hundreds of these pores, playing a crucial role in controlling the hundred of thousands of molecules that enter and exit this compartment every minute. Nuclear pores are used by many viruses to inject their genetic material into a host and they are known to change when cells become cancerous, so knowing how they work is important. Scientists understood many of the components of the nuclear pore, but exactly how those building blocks fitted together was unclear.

    “The nuclear pore is the biggest, most complicated protein complex in a human cell. We now understand how it is structured,” says Martin Beck, who led the work at EMBL. “This is a very important first step towards understanding what actually happens to nuclear pores in cancer, during ageing, and in other conditions.”

    The nuclear pore is composed of three layered rings: a nuclear ring facing the nucleus; a cytoplasmic ring facing the rest of the cell; and an inner ring in between those two. Having already pieced together how the building blocks of the nuclear and cytoplasmic rings are arranged, Martin Beck’s group at EMBL have now worked out the arrangement of the pieces that form the inner ring.

    “Surprisingly, we found that although it is made of different building blocks, the inner ring has the same basic architecture as the other two rings,” says Shyamal Mosalaganti from EMBL, who studied the ring using cryo-electron microscopy. “This very complicated structure is built using simple principles . We were able to uncover that because we interweaved a lot of different techniques here.”

    Access mp4 video here .


    Molecular architecture of the inner ring scaffold of the human nuclear pore complex

    Science team:

    Jan Kosinski1,*, Shyamal Mosalaganti1,*, Alexander von Appen1,*, Roman Teimer2, Amanda L. DiGuilio3, William Wan1, Khanh Huy Bui4, Wim J.H. Hagen1, John A. G. Briggs1,5, Joseph S. Glavy3, Ed Hurt2, Martin Beck1,5,†


    1Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
    2Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.
    3Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA.
    4Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada.
    5Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.

    ↵†Corresponding author. E-mail: martin.beck@embl.de

    ↵* These authors contributed equally to this work.

    See the full article here .

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    EMBL European Molecular Biology Laboratory campus

    EMBL is Europe’s flagship laboratory for the life sciences, with more than 80 independent groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its 1800 employees, from many nations, operate across five sites: the main laboratory in Heidelberg, and outstations in Grenoble; Hamburg; Hinxton, near Cambridge (the European Bioinformatics Institute), and Monterotondo, near Rome. Founded in 1974, EMBL is an inter-governmental organisation funded by public research monies from its member states. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Around 200 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

  • richardmitnick 5:48 pm on January 2, 2016 Permalink | Reply
    Tags: , Cell studies,   

    From ETH Zürich: “A multitool for cells” 

    ETH Zurich bloc

    ETH Zürich

    Peter Rüegg

    Cells have an infallible sense of smell that tells them which direction to grow in to move closer to the source of a scent. ETH researchers have now learned how this sense of smell works.

    Temp 1
    The polarity site (yellow traces) is a sensor, processor and motor all in one – a multifunctional instrument that controls cell growth and movement. (Graphics: ETH Zürich)

    A frequent problem faced by cells is that they are surrounded by a promising cloud of scent and must determine the direction of its source. Nerve cells, for example, form long extensions that are attracted to signals from other cells in order to produce the network that forms the nervous system; similarly, scavenger cells recognise the scent of harmful germs in order that they can pursue and destroy them.

    But how do cells sense these scent signals, which become weaker and weaker with increasing distance from the source? How do cells ‘read’ this weakening of the signal – technically referred to as a signal gradient – in order to steer their growth or movement towards the signal’s source? How spatial signals are sensed is a fundamental question facing biology – and until now this riddle has remained largely unsolved.

    Sensor, processor and motor all in one

    Now, a possible solution has been presented by researchers led by ETH Professor Matthias Peter of the Institute of Biochemistry. Yeast cells have a very fine, adjustable multitool that recognises chemical signals, processes them accordingly, and initiates the correct response – growth towards the source of the signal. Yeast cells are therefore able to smell the location of potential sexual partners in their surroundings, so that they can grow towards them.

    The biologists conducted their study using a combination of microscopic observations and a computer model that they developed through an interdisciplinary collaboration with researchers from the Automatic Control Lab under Heinz Koeppl (now at TU Darmstadt).

    Many proteins form multi tool

    If the cell suspects that a signal gradient is nearby, it assembles the multitool at a random position on the membrane. This tool is a large protein complex made up of more than 100 different components; the complex is so big that it can be seen through a fluorescence microscope. The researchers call this a ‘polarity site’ (PS) because polarised growth sets in at the location where it forms.

    Using fluorescence microscopy, the researchers have now observed how the PS locates a gradient’s signal source. First, the PS moves along the membrane towards the stronger signal. Once it has identified the strongest signal – i.e. the largest amount of signal substance in the gradient – it stops moving. The PS then creates a bulge in the cell at this location, which continues to grow towards the source of the signal. Naturally, the signal is produced by a sexual partner and the two cells fuse once they have found one another.

    Complex structure reduced using a model

    In order to understand the molecular mechanics of this process, the researchers referred to the computer model. “This model really helped us to reduce the complexity of the PS and the process to a few essential components,” says Björn Hegemann, lead author of a study published in the journal Development Cell. These essential components of the machinery include a receptor that picks up and forwards the signal; others include the protein Cdc42, which carries the receptor along the membrane, and the protein Cdc24, which regulates the activity of Cdc42. “You could describe the receptor as the nose, Cdc42 as the wheel of the machinery and Cdc24 as its brake,” says Hegemann.

    While the PS is moving across the cell membrane and looking for a stronger chemical signal, only a few molecules of the breaking protein Cdc24 are present in the machinery. Once it has found the signal’s maximum concentration, the PS requests additional Cdc24 molecules, which are stored in the nucleus, to bind to the complex. The more Cdc24 molecules that attach to the PS machine, the slower it becomes. However, only when Cdc24 numbers exceeds a certain threshold does the PS stop completely and start the bulge formation in the cell.

    An important foundation stone

    “First, we observed the polarity site’s movement using the fluorescence microscope. Then we simulated this movement on the computer, which allowed us to develop a hypothesis for how the movement could be controlled. We were then able to confirm this hypothesis experimentally through mutations and using the fluorescence microscope,” says Hegemann, who is pleased with the new findings. He says the relatively simple computer model provided an excellent basis for planning the experiments by enabling the researchers to change the components rapidly and thereby identify important aspects. This made the study simpler, he says, as it was not necessary to test everything experimentally.

    Hegemann assumes that it’s not only yeast cells that use a multitool resembling the polarity site. Behaviour similar to that of a PS has also been observed in fission yeast (S. pombe) and the roundworm (C. elegans), albeit with no molecular explanation. The ETH researchers have now provided this explanation and described in detail for the first time how cells can locate a scent gradient. This work lays an important foundation stone for further studies on spatial signal perception by cells – both in yeast and in humans. According to Hegemann, currently no direct medical applications are envisaged: “In the distant future, this work might well benefit the general public. At the moment, however, it primarily represents an important advance for fundamental research.”


    Hegemann B, Unger M, Lee SS, Stoffel-Studer I, van den Heuvel J, Pelet S, Koeppl H, Peter M. A Cellular System for Spatial Signal Decoding in Chemical Gradients. Developmental Cell, Volume 35, Issue 4, 23 November 2015, Pages 458–470. DOI: 10.1016/j.devcel.2015.10.013

    See the full article here .

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    ETH Zurich campus
    ETH Zurich is one of the leading international universities for technology and the natural sciences. It is well known for its excellent education, ground-breaking fundamental research and for implementing its results directly into practice.

    Founded in 1855, ETH Zurich today has more than 18,500 students from over 110 countries, including 4,000 doctoral students. To researchers, it offers an inspiring working environment, to students, a comprehensive education.

    Twenty-one Nobel Laureates have studied, taught or conducted research at ETH Zurich, underlining the excellent reputation of the university.

  • richardmitnick 4:30 pm on September 17, 2015 Permalink | Reply
    Tags: , , Cell studies, ,   

    From UCSD and Scripps: “UC San Diego and TSRI Launch New Consortium to Create ‘Virtual Cell’” 

    UC San Diego bloc

    UC San Diego

    Scripps Institute
    Scripps Research Institute

    Credit: Art Olson and TSRI

    Drawing on complementary strengths, the University of California, San Diego and The Scripps Research Institute have formed a new consortium with a big mission: to map cells in space and time.

    The consortium will offer fellowship funding for 10 to 12 graduate students and postdoctoral fellows to work on collaborative projects that build bridges between the campuses and different disciplines to assemble and simulate a virtual model of a cell, down to an atomic level of detail.

    “Leveraging existing strengths at UC San Diego and Scripps, the collaboration will advance scientific excellence and research infrastructure at both institutions,” said UC San Diego Chancellor Pradeep K. Khosla. “The goal of building virtual cells poses an important challenge to researchers in fields from experimental biology to computation and information analysis.”

    “We are entering into this promising collaboration between our campuses with great optimism,” said TSRI Acting President and CEO Jim Paulson. “The Visible Molecular Cell Consortium aims to bring together the best minds from different disciplines to understand and articulate how the body’s cells work, which will lay important groundwork to understanding health and disease.”

    The Visible Molecular Cell Consortium will be directed jointly by Art Olson, professor at TSRI and Rommie Amaro, associate professor of chemistry and biochemistry at UC San Diego.

    “This is a particularly exciting time for such efforts, due to a number of technological and scientific factors,” said Amaro. “Advances in various imaging technologies, modeling frameworks and cyber-infrastructure are enabling us to make new strides in the creation of 3D virtual cells. This timely new inter-institutional alliance will provide new insights into the inner workings of cell machinery, some of which may present opportunities for novel therapeutics.”

    In recent years, more powerful imaging devices and automated programs in high resolution imaging have provided more detailed pictures of cells and their proteins than ever before, but scientists have not yet translated the huge amounts of data into a single, atomic-level cellular model. This is a “big data” challenge, Olson points out, applied to the uncharted territory of cellular architecture and ecology.

    “Even the simplest living cells contain 1 to 2 million proteins, of 3,000 to 4,000 different types,” said Olson. “Figuring out how they work together over time will shed light on the cell as a living, working individual entity. Just like you couldn’t build a car from just its wiring diagram, we can’t have a complete understanding of a cell unless we know how all of its physical parts work together in 3D.”

    The researchers hope to one day be able to zoom into cells at the atomic level and zoom out to see “nano neighborhoods,” where cells interact. On top of that, they aim to visualize protein interactions in real time to better understand cellular function. The new consortium will help scientists put the pieces together.

    TSRI is known for its structural biology using both cryo-electron microscopy and X-ray crystallography, and both Olson’s and Amaro’s labs develop and use advanced graphics programs to visualize complex cellular machinery. UC San Diego is home to the only publicly available supercomputer in California and the National Biomedical Computation Resource, a National Institutes of Health-sponsored national resource that develops multi-scale modeling tools.

    Olson and Amaro plan to host their first “lightning talk” workshop, where any scientist can present their work and seek out collaborators, on Oct. 2. They also plan to organize a bi-annual conference to encourage new collaborations and share results. Researchers interested in learning more about the consortium are encouraged to contact visiblemolecularcell@gmail.com.

    The organizers anticipate the consortium will be particularly strong in neurological diseases and infectious diseases, such as influenza, HIV and Ebola virus, although the insights into cellular behavior will be applicable across many fields.

    See the full article here .

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    UC San Diego Campus

    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

    Scripps Institute Campus

    The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

  • richardmitnick 7:15 pm on August 27, 2015 Permalink | Reply
    Tags: , , Cell studies   

    From Caltech: “Caltech Chemists Solve Major Piece of Cellular Mystery” 

    Caltech Logo

    Kimm Fesenmaier

    Team determines the architecture of a second subcomplex of the nuclear pore complex [NPC]

    Credit: Lance Hayashida/Caltech and the Hoelz Laboratory/Caltech

    Credit: Hoelz Laboratory/Caltech

    Not just anything is allowed to enter the nucleus, the heart of eukaryotic cells where, among other things, genetic information is stored. A double membrane, called the nuclear envelope, serves as a wall, protecting the contents of the nucleus.

    Human cell nucleus

    Any molecules trying to enter or exit the nucleus must do so via a cellular gatekeeper known as the nuclear pore complex (NPC), or pore, that exists within the envelope.

    How can the NPC be such an effective gatekeeper—preventing much from entering the nucleus while helping to shuttle certain molecules across the nuclear envelope? Scientists have been trying to figure that out for decades, at least in part because the NPC is targeted by a number of diseases, including some aggressive forms of leukemia and nervous system disorders such as a hereditary form of Lou Gehrig’s disease. Now a team led by André Hoelz, assistant professor of biochemistry at Caltech, has solved a crucial piece of the puzzle.

    In February of this year, Hoelz and his colleagues published a paper describing the atomic structure of the NPC’s coat nucleoporin complex, a subcomplex that forms what they now call the outer rings (see illustration). Building on that work, the team has now solved the architecture of the pore’s inner ring, a subcomplex that is central to the NPC’s ability to serve as a barrier and transport facilitator. In order to the determine that architecture, which determines how the ring’s proteins interact with each other, the biochemists built up the complex in a test tube and then systematically dissected it to understand the individual interactions between components. Then they validated that this is actually how it works in vivo, in a species of fungus.

    For more than a decade, other researchers have suggested that the inner ring is highly flexible and expands to allow large macromolecules to pass through. “People have proposed some complicated models to explain how this might happen,” says Hoelz. But now he and his colleagues have shown that these models are incorrect and that these dilations simply do not occur.

    “Using an interdisciplinary approach, we solved the architecture of this subcomplex and showed that it cannot change shape significantly,” says Hoelz. “It is a relatively rigid scaffold that is incorporated into the pore and basically just sits as a decoration, like pom-poms on a bicycle. It cannot dilate.”

    The new paper appears online ahead of print on August 27 in Science Express. The four co-lead authors on the paper are Caltech postdoctoral scholars Tobias Stuwe, Christopher J. Bley, and Karsten Thierbach, and graduate student Stefan Petrovic.

    Together, the inner and outer rings make up the symmetric core of the NPC, a structure that includes 21 different proteins. The symmetric core is so named because of its radial symmetry (the two remaining subcomplexes of the NPC are specific to either the side that faces the cell’s cytoplasm or the side that faces the nucleus and are therefore not symmetric). Having previously solved the structure of the coat nucleoporin complex and located it in the outer rings, the researchers knew that the remaining components that are not membrane anchored must make up the inner ring.

    They started solving the architecture by focusing on the channel nucleoporin complex, or channel, which lines the central transport channel and is made up of three proteins, accounting for about half of the inner ring. This complex produces filamentous structures that serve as docking sites for specific proteins that ferry molecules across the nuclear envelope.

    The biochemists employed bacteria to make the proteins associated with the inner ring in a test tube and mixed various combinations until they built the entire subcomplex. Once they had reconstituted the inner ring subcomplex, they were able to modify it to investigate how it is held together and which of its components are critical, and to determine how the channel is attached to the rest of the pore.

    Hoelz and his team found that the channel is attached at only one site. This means that it cannot stretch significantly because such shape changes require multiple attachment points. Hoelz notes that a new electron microscopy study of the NPC published in 2013 by Martin Beck’s group at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, indicated that the central channel is bigger than previously thought and wide enough to accommodate even the largest cargoes known to pass through the pore.

    When the researchers introduced mutations that effectively eliminated the channel’s single attachment, the complex could no longer be incorporated into the inner ring. After proving this in the test tube, they also showed this to be true in living cells.

    “This whole complex is a very complicated machine to assemble. The cool thing here is that nature has found an elegant way to wait until the very end of the assembly of the nuclear pore to incorporate the channel,” says Hoelz. “By incorporating the channel, you establish two things at once: you immediately form a barrier and you generate the ability for regulated transport to occur through the pore.” Prior to the channel’s incorporation, there is simply a hole through which macromolecules can freely pass.

    Next, Hoelz and his colleagues used X-ray crystallography to determine the structure of the channel nucleoporin subcomplex bound to the adaptor nucleoporin Nic96, which is its only nuclear pore attachment site. X-ray crystallography involves shining X-rays on a crystallized sample and analyzing the pattern of rays reflected off the atoms in the crystal. Because the NPC is a large and complex molecular machine that also has many moving parts, they used an engineered antibody to essentially “superglue” many copies of the complex into place to form a nicely ordered crystalline sample. Then they analyzed hundreds of samples using Caltech’s Molecular Observatory—a facility developed with support from the Gordon and Betty Moore Foundation that includes an automated X-ray beam line at the Stanford Synchrotron Radiation Laboratory that can be controlled remotely from Caltech—and the GM/CA beam line at the Advanced Photon Source at the Argonne National Laboratory. Eventually, they were able to determine the size, shape, and position of all the atoms of the channel nucleoporin subcomplex and its location within the full NPC.

    “The crystal structure nailed it,” Hoelz says. “There is no way that the channel is changing shape. All of that other work that, for more than 10 years, suggested it was dilating was wrong.”

    The researchers also solved a number of crystal structures from other parts of the NPC and determined how they interact with components of the inner ring. In doing so they demonstrated that one such interaction is critical for positioning the channel in the center of the inner ring. They found that exact positioning is needed for the proper export from the nucleus of mRNA and components of ribosomes, the cell’s protein-making complexes, rendering it critical in the flow of genetic information from DNA to mRNA to protein.

    Hoelz adds that now that the architectures of the inner and outer rings of the NPC are known, getting an atomic structure of the entire symmetric core is “a sprint to the summit.”

    “When I started at Caltech, I thought it might take another 10, 20 years to do this,” he says. “In the end, we have really only been working on this for four and a half years, and the thing is basically tackled. I want to emphasize that this kind of work is not doable everywhere. The people who worked on this are truly special, talented, and smart; and they worked day and night on this for years.”

    Ultimately, Hoelz says he would like to understand how the NPC works in great detail so that he might be able to generate therapies for diseases associated with the dysfunction of the complex. He also dreams of building up an entire pore in the test tube so that he can fully study it and understand what happens as it is modified in various ways. “Just as they did previously when I said that I wanted to solve the atomic structure of the nuclear pore, people will say that I’m crazy for trying to do this,” he says. “But if we don’t do it, it is likely that nobody else will.”

    The paper, “Architecture of the fungal nuclear pore inner ring complex,” had a number of additional Caltech authors: Sandra Schilbach (now of the Max Planck Institute of Biophysical Chemistry), Daniel J. Mayo, Thibaud Perriches, Emily J. Rundlet, Young E. Jeon, Leslie N. Collins, Ferdinand M. Huber, and Daniel H. Lin. Additional coauthors include Marcin Paduch, Akiko Koide, Vincent Lu, Shohei Koide, and Anthony A. Kossiakoff of the University of Chicago; and Jessica Fischer and Ed Hurt of Heidelberg University.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 4:09 pm on February 12, 2015 Permalink | Reply
    Tags: , , Cell studies   

    From Caltech: “Caltech biochemist sheds light on structure of key cellular ‘gatekeeper'” 

    Caltech Logo

    Jon Nalick


    Facing a challenge akin to solving a 1,000-piece jigsaw puzzle while blindfolded—and without touching the pieces—many structural biochemists thought it would be impossible to determine the atomic structure of a massive cellular machine called the nuclear pore complex (NPC), which is vital for cell survival.

    But after 10 years of attacking the problem, a team led by André Hoelz, assistant professor of chemistry, recently solved almost a third of the puzzle. The approach his team developed to do so also promises to speed completion of the remainder.

    In an article published online February 12 by Science Express, Hoelz and his colleagues describe the structure of a significant portion of the NPC, which is made up of many copies of about 34 different proteins, perhaps 1,000 proteins in all and a total of 10 million atoms. In eukaryotic cells (those with a membrane-bound nucleus), the NPC forms a transport channel in the nuclear membrane. The NPC serves as a gatekeeper, essentially deciding which proteins and other molecules are permitted to pass into and out of the nucleus. The survival of cells is dependent upon the accuracy of these decisions.

    Understanding the structure of the NPC could lead to new classes of cancer drugs as well as antiviral medicines. “The NPC is a huge target of viruses,” Hoelz says. Indeed, pathogens such as HIV and Ebola subvert the NPC as a way to take control of cells, rendering them incapable of functioning normally. Figuring out just how the NPC works might enable the design of new drugs to block such intruders.

    “This is an incredibly important structure to study,” he says, “but because it is so large and complex, people thought it was crazy to work on it. But 10 years ago, we hypothesized that we could solve the atomic structure with a divide-and-conquer approach—basically breaking the task into manageable parts—and we’ve shown that for a major section of the NPC, this actually worked.”

    To map the structure of the NPC, Hoelz relied primarily on X-ray crystallography, which involves shining X-rays on a crystallized sample and using detectors to analyze the pattern of rays reflected off the atoms in the crystal.

    It is particularly challenging to obtain X-ray diffraction images of the intact NPC for several reasons, including that the NPC is both enormous (about 30 times larger than the ribosome, a large cellular component whose structure wasn’t solved until the year 2000) and complex (with as many as 1,000 individual pieces, each composed of several smaller sections). In addition, the NPC is flexible, with many moving parts, making it difficult to capture in individual snapshots at the atomic level, as X-ray crystallography aims to do. Finally, despite being enormous compared to other cellular components, the NPC is still vanishingly small (only 120 nanometers wide, or about 1/900th the thickness of a dollar bill), and its highly flexible nature prohibits structure determination with current X-ray crystallography methods.

    To overcome those obstacles, Hoelz and his team chose to determine the structure of the coat nucleoporin complex (CNC)—one of the two main complexes that make up the NPC—rather than tackling the whole structure at once (in total the NPC is composed of six subcomplexes, two major ones and four smaller ones, see illustration). He enlisted the support of study coauthor Anthony Kossiakoff of the University of Chicago, who helped to develop the engineered antibodies needed to essentially “superglue” the samples into place to form an ordered crystalline lattice so they could be properly imaged. The X-ray diffraction data used for structure determination was collected at the General Medical Sciences and National Cancer Institutes Structural Biology Beamline at the Argonne National Laboratory.

    With the help of Caltech’s Molecular Observatory—a facility, developed with support from the Gordon and Betty Moore Foundation, that includes a completely automated X-ray beamline at the Stanford Synchrotron Radiation Laboratory that can be controlled remotely from Caltech—Hoelz’s team refined the antibody adhesives required to generate the best crystalline samples. This process alone took two years to get exactly right.

    Hoelz and his team were able to determine the precise size, shape, and the position of all atoms of the CNC, and also its location within the entire NPC.

    The CNC is not the first component of the NPC to be fully characterized, but it is by far the largest. Hoelz says that once the other major component—known as the adaptor–channel nucleoporin complex—and the four smaller subcomplexes are mapped, the NPC’s structure will be fully understood.

    The CNC that Hoelz and his team evaluated comes from baker’s yeast—a commonly used research organism—but the CNC structure is the right size and shape to dock with the NPC of a human cell. “It fits inside like a hand in a glove,” Hoelz says. “That’s significant because it is a very strong indication that the architecture of the NPC in both are probably the same and that the machinery is so important that evolution has not changed it in a billion years.”

    Being able to successfully determine the structure of the CNC makes mapping the remainder of the NPC an easier proposition. “It’s like climbing Mount Everest. Knowing you can do it lowers the bar, so you know you can now climb K2 and all these other mountains,” says Hoelz, who is convinced that the entire NPC will be characterized soon. “It will happen. I don’t know if it will be in five or 10 or 20 years, but I’m sure it will happen in my lifetime. We will have an atomic model of the entire nuclear pore.”

    Still, he adds, “My dream actually goes much farther. I don’t really want to have a static image of the pore. What I really would like—and this is where people look at me with a bit of a smile on their face, like they’re laughing a little bit—is to get an image of how the pore is moving, how the machine actually works. The pore is not a static hole, it can open up like the iris of a camera to let something through that’s much bigger. How does it do it?”

    To understand that machine in motion, he adds, “you don’t just need one snapshot, you need multiple snapshots. But once you have one, you can infer the other ones much quicker, so that’s the ultimate goal. That’s the dream.”

    Along with Hoelz, additional Caltech authors on the paper, Architecture of the Nuclear Pore Complex Coat, include postdoctoral scholars Tobias Stuwe and Ana R. Correia, and graduate student Daniel H. Lin. Coauthors from the University of Chicago Department of Biochemistry and Molecular Biology include Anthony Kossiakoff, Marcin Paduch and Vincent Lu. The work was supported by Caltech startup funds, the Albert Wyrick V Scholar Award of the V Foundation for Cancer Research, the 54th Mallinckrodt Scholar Award of the Edward Mallinckrodt, Jr. Foundation, and a Kimmel Scholar Award of the Sidney Kimmel Foundation for Cancer Research.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 4:27 pm on January 29, 2015 Permalink | Reply
    Tags: , Cell studies,   

    From SLAC: “X-ray Study Reveals Division of Labor in Cell Health Protein” 

    SLAC Lab

    January 28, 2015
    Identical Substructures in ‘TH Protein’ Couple Two Crucial Cellular Functions

    A recent study performed in part at SLAC’s SSRL X-ray facility has provided new insights into how the critical mitochondrial enzyme transhydrogenase, or TH, works in a key process that maintains healthy cells. The crystal structure of TH shows two copies of the molecule (left and right), each of which contains three domains (I, II, III). Structural asymmetry is observed for domain III: One of the structures is facing up (green) to catalyze the production of NADPH from its precursor (black spheres); the other is facing down (magenta) towards the transmembrane domain II to facilitate the transit of a proton. Labels “in” and “out” denote the mitochondrial matrix and the space outside the inner mitochondrial membrane, respectively. (C. David Stout/The Scripps Research Institute)

    Researchers working in part at the Department of Energy’s SLAC National Accelerator Laboratory have discovered that a key protein for cell health, which has recently been linked to diabetes, cancer and other diseases, can multitask by having two identical protein parts divide labor.

    The TH enzyme, short for transhydrogenase, is a crucial protein for most forms of life. In humans and other higher organisms, it works within mitochondria – tiny, double-hulled oxygen reactors inside cells that help power most cellular processes.

    “Despite its importance, TH has been one of the least studied mitochondrial enzymes,” said C. David Stout, a scientist at The Scripps Research Institute whose group led the research. The new study, published Jan. 9 in Science, is an important step toward understanding how this protein manages to perform two crucial cellular tasks at the same time.

    Two Crucial Processes

    As a mitochondrion burns oxygen, it pumps protons out of its innermost compartment, or matrix. Part of the TH protein extends through the membrane that surrounds the matrix; it allows a one-by-one flow of protons back through the membrane. This proton influx, in turn, is linked to the production of NADPH, a compound crucial for defusing oxygen radicals that are harmful to cells.

    But how do TH enzymes couple proton transport and NADPH production? Although Stout’s laboratory and others have previously described portions of the TH enzyme that protrude from the membrane into the mitochondrial matrix, a precise understanding of TH’s mechanism has been elusive. The enzyme has an exceptionally loose structure that makes it hard to evaluate by X-ray crystallography, the standard tool for determining structures of large proteins.

    “Key details we’ve been lacking include the structure of TH’s transmembrane portion, and the way in which the parts assemble into the whole enzyme,” said Josephine H. Leung, a graduate student in the Stout laboratory who was the lead author of the new study.

    For the first time, the team was now able to determine precise details of the transmembrane portion using X-rays from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) and Argonne National Laboratory’s Advanced Photon Source (APS), both DOE Office of Science User Facilities. Together with X-ray and electron microscopy data of the whole protein, the study provided major clues as to how TH works.


    ANL APS interior

    Flipping Functions

    The analysis revealed that two identical copies of TH are bound together in what is called a dimer, and that one copy appears to be involved in proton transport while the other takes part in NADPH production. “Our new study helps clear up some mysteries – suggesting how the enzyme structure might harness protons and indicating that its two sides are able to alternate functions, always staying in balance,” Stout said.

    Attached to TH’s transmembrane structure, just inside the mitochondrial matrix, is the “domain III” structure, which binds NADPH’s precursor molecule during NADPH synthesis. Previously, scientists did not understand how two such structures could work side by side in the TH dimer and not interfere with each other’s activity.

    The new data suggest that these side-by-side structures are highly flexible and always have different orientations.

    “Our most striking finding was that the two domain III structures are not symmetric – one of them faces up while the other faces down,” said Leung.

    In particular, one of the structures is apparently oriented to catalyze the production of NADPH, while the other is turned towards the membrane, perhaps to facilitate transit of a proton. The new structural model indicates that with each proton transit, the two domain III structures flip and switch their functions. “We suspect that the passage of the proton is what somehow causes this flipping of the domain III structures,” said Leung.

    But much work remains to be done to determine TH’s precise structure and mechanism. For example, the new structural data provide evidence of a likely proton channel in the TH transmembrane region, but show only a closed conformation of that structure. “We suspect that this channel can have another, open conformation that lets the proton pass through, so that’s one of the details we want to study further,” said Leung.

    Research funding for the SSRL Structural Molecular Biology Program was provided by the DOE Office of Biological and Environmental Research and the National Institutes of Health, National Institute of General Medical Sciences.

    See the full article here.

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    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

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