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  • richardmitnick 4:16 am on May 7, 2014 Permalink | Reply
    Tags: , , , Protein Studies,   

    From APS at Agonne Lab: “Advanced Photon Source to remain leader in protein structure research for years” 

    News from APS at Argonne National Laboratory

    May 5, 2014
    Brian Grabowski

    Proteins are involved in virtually every process in all living cells on the planet, be it a bacterium or yourself. In humans, antibodies defend against invading bacteria, viruses and other infectious agents. Insulin helps regulate how your body uses carbohydrates and fats. Lactase helps digest lactose from dairy products.

    ps
    The world’s first protein characterization research facility directly attached to a light source will open in the near future at the Advanced Photon Source. The Advanced Protein Characterization Facility will use state-of-the-art robotics for gene cloning, protein expression, protein purification and protein crystallization.

    But scientists know the structures and functions of only a small fraction of the proteins in living systems. The vast majority remain a mystery. The backlog of uncharacterized proteins grows quickly every day as scientists continue to determine the genetic makeups of thousands of new organisms, using astonishingly efficient techniques of genome sequencing.

    No X-ray facility in the world has supported more protein structure research and characterized more proteins than the Advanced Photon Source (APS) at the U.S. Department of Energy’s Argonne National Laboratory. Soon this 2/3-mile-in-circumference X-ray instrument will get a boost in efficiency that likely will translate into a big boon for the discovery of new pharmaceuticals and the control of genetic disorders and other diseases, as well as advancing the biotech industry.

    The world’s first protein characterization research facility directly attached to a light source will open in the near future at the APS. The Advanced Protein Characterization Facility (APCF) will use state-of-the-art robotics for gene cloning, protein expression, protein purification and protein crystallization.

    robotics
    Not beautiful, but very efficient

    “The net result will be more protein structures analyzed per year, higher resolution structures and more research into protein function,” said Andrzej Joachimiak, an Argonne Distinguished Fellow who also is director of the Structural Biology Center’s (SBC’s) Sector 19 beamlines and the Midwest Center for Structural Genomics. “This facility has been designed to integrate systems biology and molecular biology with gene cloning, protein expression, protein purification, protein crystallization and crystal testing and delivery to the APS. There is nothing like this anywhere in the world right now.”

    When a new protein structure is discovered and verified, the data are deposited in the Protein Data Bank repository to make it available to researchers around the world. For the last 11 consecutive years, the APS has been far and away the world leader in protein structure deposits. The APS has 14 beamlines dedicated to the study of protein crystals through a technique called macromolecular crystallography.

    “Two Nobel Prizes for Chemistry were awarded in the past four years for APS-based research involving crystallography,” said Joachimiak, “One Nobel Prize was for research into the structure and function of ribosomes on SBC’s 19-ID beamline, and another was awarded in 2012 for studies of G-protein-coupled receptors at a GM/CA-CAT micro-focus beamline.”

    Ribosomes make proteins in all living cells. Improved knowledge about bacterial ribosomes, for example, is speeding development of new antibiotics that combat bacterial infections by interfering with protein production. G-protein-coupled receptor (GPCR) proteins help cells stay in constant communication with each other, thereby facilitating resource sharing. When normal cells become cancerous, GPCRs are changed, too. The change can corrupt the lines of communication, allowing the cancerous cells to grow without limits. The first discovery of the structure of a human GPCR was made at the APS as part of the Nobel Prize-winning research. In fact, the structure was captured at the exact moment the GPCR was signaling across a cell membrane.

    The APCF will be available for use by the more than 5,500 scientists who visit the APS annually, but it will have a particularly strong connection to Argonne’s SBC and the beamline it operates at Sector 19. In 2013, more than 660 crystallographers used the SBC facility to collect data on hundreds of projects, including proteins from the Ebola virus. More than 4,100 protein structures have been deposited into the Protein Data Bank from SBC.

    Protein structures are analyzed by crystalling the proteins and then placing the single crystals into an X-ray beam for analysis using X-ray diffraction. The results depend on the quality of both the protein crystal and the X-ray beam. The APS provides some of the most brilliant X-ray beams in the Western Hemisphere. Additionally, the APS generates a highly parallel beam, which enables tight focusing of the X-rays. Staff at the National Institute of General Medical Sciences and National Cancer Institute structural biology facility (GM/CA-CAT) beamline capitalized on this and created the world’s first micro X-ray beam at the request of visiting researchers. “The micro-beam was essential for the GPCR research,” said Joachimiak.

    The crystallography capabilities of the APS will increase with a planned upgrade. “After the upgrade, the brilliance of the X-ray beam will increase by two to three orders of magnitude,” Joachimiak said. “The beam will be more parallel, too, so we will be able to focus down to a very small beam size. This beam will also be two to three times more intense. The upgrade should help ensure APS leadership in macromolecular crystallography for many years to come.”

    See the full article here.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security.

    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

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  • richardmitnick 4:16 pm on March 21, 2014 Permalink | Reply
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    From Argonne APS: “A Layered Nanostructure Held Together By DNA” 

    News from Argonne National Laboratory

    March 18, 2014
    David Lindley

    Dreaming up nanostructures that have desirable optical, electronic, or magnetic properties is one thing. Figuring out how to make them is another. A new strategy uses the binding properties of complementary strands of DNA to attach nanoparticles to each other and builds up a layered thin-film nanostructure through a series of controlled steps. Investigation at the U.S. Department of Energy Office of Science’s Advanced Photon Source has revealed the precise form that the structures adopted, and points to ways of exercising still greater control over the final arrangement.

    dna
    DNA

    The idea of using DNA to hold nanoparticles was devised more than 15 years ago by Chad Mirkin and his research team at Northwestern University. They attached short lengths of single-stranded DNA with a given sequence to some nanoparticles, and then attached DNA with the complementary sequence to others. When the particles were allowed to mix, the “sticky ends” of the DNA hooked up with each other, allowing for reversible aggregation and disaggregation depending on the hybridization properties of the DNA linkers.

    sticky
    Nanoparticles linked by complementary DNA strands form a bcc superlattice when added layer-by-layer to a DNA coated substrate. When the substrate DNA is all one type, the superlattice forms at a different orientation (top row) than if the substrate has both DNA linkers (bottom row). GISAXS scattering patterns (right) and scanning electron micrographs (inset) reveal the superlattice structure. No image credit.

    Recently, this DNA “smart glue” has been utilized to assemble nanoparticles into ordered arrangements resembling atomic crystal lattices, but on a larger scale. To date, nanoparticle superlattices have been synthesized in well over 100 crystal forms, including some that have never been observed in nature.

    However, these superlattices are typically polycrystalline, and the size, number, and orientation of the crystals within them is generally unpredictable. To be useful as metamaterials, photonic crystals, and the like, single superlattices with consistent size and fixed orientation are needed.

    Northwestern researchers and a colleague at Argonne National Laboratory have devised a variation on the DNA-linking procedure that allows a greater degree of control.

    The basic elements of the superlattice were gold nanoparticles, each 10 nanometers across. These particles were made in two distinct varieties, one adorned with approximately 60 DNA strands of a certain sequence, while the other carried the complementary sequence.

    The researchers built up thin-film superlattices on a silicon substrate that was also coated with DNA strands. In one set of experiments, the substrate DNA was all of one sequence – call it the “B” sequence – and it was first dipped into a suspension of nanoparticles with the complementary “A” sequence.

    When the A and B ends connected, the nanoparticles formed a single layer on the substrate. Then the process was repeated with a suspension of the B-type nanoparticles, to form a second layer. The whole cycle was repeated, as many as four more times, to create a multilayer nanoparticle superlattice in the form of a thin film.

    Grazing incidence small-angle x-ray scattering (GISAXS) studies carried out at the X-ray Science Division 12-ID-B beamline at the Argonne Advanced Photon Source revealed the symmetry and orientation of the superlattices as they formed. Even after just three half-cycles, the team found that the nanoparticles had arranged themselves into a well-defined, body-centered cubic (bcc) structure, which was maintained as more layers were added.

    In a second series of experiments, the researchers seeded the substrate with a mix of both the A and B types of DNA strand. Successive exposure to the two nanoparticle types produced the same bcc superlattice, but with a different vertical orientation. That is, in the first case, the substrate lay on a plane through the lattice containing only one type of nanoparticle, while in the second case, the plane contained an alternating pattern of both types (see the figure).

    To get orderly superlattice growth, the researchers had to conduct the process at the right temperature. Too cold, and the nanoparticles would stick to the substrate in an irregular fashion, and remain stuck. Too hot, and the DNA linkages would not hold together.

    But in a temperature range of a couple of degrees on either side of about 40° C (just below the temperature at which the DNA sticky ends detach from each other), the nanoparticles were able to continuously link and unlink from each other. Over a period of about an hour per half-cycle, they settled into the bcc superlattice, the most thermodynamically stable arrangement.

    GISAXS also revealed that although the substrate forced superlattices into specific vertical alignments, it allowed the nanoparticle crystals to form in any horizontal orientation. The researchers are now exploring the possibility that by patterning the substrate in a suitable way, they can control the orientation of the crystals in both dimensions, increasing the practical value of the technique.

    See the full article here.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security.

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  • richardmitnick 3:47 pm on March 21, 2014 Permalink | Reply
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    From Brookhaven Lab: “Understanding the Initiation of Protein Synthesis in Mammals” 

    Brookhaven Lab

    March 18, 2014
    Chelsea Whyte

    Protein synthesis, the process by which cells generate new proteins, is the most important cellular function, requiring more than 70 percent of the total energy of a cell. The initiation of this process is the most regulated and most critical component, but it is still the least understood.

    protein
    Messenger RNA (in red) latches closed around a pre-initiation complex, and attaches to transfer RNA (in green), beginning a process of protein synthesis specific to eukaryotes — animals, plants, and fungi.

    Research by Ivan Lomakin and Thomas Steitz of Yale University has unlocked the genetic scanning mechanism that begins this crucial piece of cell machinery.

    They determined the structures of three complexes of the ribosome, a complex molecular machine that links together amino acids to form proteins according to an order specified by messenger RNA. These three structures represent distinct steps in protein translation in mammals – the recruitment and scanning of mRNA, the selection of initiator tRNA, and the joining of large and small ribosomal subunits.

    “Any small defect or disruption in the protein synthesis process can cause abnormalities or disease,” said Lomakin. “Understanding this process is critical for understanding how human life comes to be, and how some over-expressions or abnormalities in the initiation of protein synthesis may be connected to cancer or Alzheimer’s or other diseases.”

    Using x-ray crystallography on ribosomal subunits purified from rabbit cells, they were able to determine the positions and roles of the different pieces of cellular machinery, a bit like creating a playbook for a football game. They found that the tRNA and mRNA compete for position at the P site – one of three key sites on a ribosome – where short chains of amino acids are linked to form proteins.

    “Now, we have a low resolution structure, so we can’t yet talk about atomic details of the mechanism,” said Lomakin. “The next important step is to get higher resolution images. And we can change organisms to see if they behave differently, so we’re working on the structure of human ribosome initiation complexes, too.”

    For this higher resolution, Lomakin and his collaborators will use the National Synchrotron Light Source II, a new state-of-the-art light source that will begin early science at Brookhaven National Laboratory in 2014. “Our hope is to be able to look at very weak diffraction to get higher resolution structures of these important cellular mechanisms.”

    Brookhaven NSLS II Photo
    NSLS-II at Brookhaven Lab

    See the full article here.

    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 2:21 pm on March 17, 2014 Permalink | Reply
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    From Berkeley Lab: “Bright Future for Protein Nanoprobes” 


    Berkeley Lab

    March 17, 2014
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    The term a “brighter future” might be a cliché, but in the case of ultra-small probes for lighting up individual proteins, it is now most appropriate. Researchers at the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) have discovered surprising new rules for creating ultra-bright light-emitting crystals that are less than 10 nanometers in diameter. These ultra-tiny but ultra-bright nanoprobes should be a big asset for biological imaging, especially deep-tissue optical imaging of neurons in the brain.

    Working at the[Berkeley Lab's] Molecular Foundry, a DOE national nanoscience center hosted at Berkeley Lab, a multidisciplinary team of researchers led by James Schuck and Bruce Cohen, both with Berkeley Lab’s Materials Sciences Division, used advanced single-particle characterization and theoretical modeling to study what are known as “upconverting nanoparticles” or UCNPs. Upconversion is the process by which a molecule absorbs two or more photons at a lower energy and emits them at higher energies. The research team determined that the rules governing the design of UCNP probes for ensembles of molecules do not apply to UCNP probes designed for single-molecules.

    “The widely accepted conventional wisdom for designing bright UCNPs has been that you want to use a high concentration of sensitizer ions and a relatively small concentration of emitter ions, since too many emitters will result in self-quenching that leads to lower brightness, says Schuck, who directs the Molecular Foundry’s Imaging and Manipulation of Nanostructures Facility. “Our results show that under the higher excitation powers used for imaging single particles, emitter concentrations should be as high as possible without compromising the structure of the nanocrystal, while sensitizer content can potentially be eliminated.”

    four
    From left Bruce Cohen, Emory Chan, Dan Gargas and Jim Schuck led a study at the Molecular Foundry to develop ultra-small, ultra-bright nanoprobes that should be a big asset for biological imaging, especially imaging neurons in the brain. (Photo by Roy Kaltschmidt)

    Schuck and Cohen are the corresponding authors of a paper describing this research in Nature Nanotechnology. The paper is titled Engineering bright sub-10-nm upconverting nanocrystals for single-molecule imaging. Co-authors are Daniel Gargas, Emory Chan, Alexis Ostrowski, Shaul Aloni, Virginia Altoe, Edward Barnard, Babak Sanii, Jeffrey Urban and Delia Milliron.

    Proteins are one of the fundamental building blocks of biology. The cells that make up tissues and organs are constructed from assemblies of proteins interacting with other biomolecules, while other proteins control nearly every chemical process inside a cell. Studying the location, assembly, and movement of specific proteins is essential for understanding how cells function and what goes wrong in diseased cells. Scientists often study proteins within cells by labeling them with light-emitting probes, but finding probes that are bright enough for imaging but not so large as to disrupt the protein’s function has been a challenge. Fluorescent organic dye molecules and semiconductor quantum dots meet the size requirements but impose other limitations.

    “Organic dyes and quantum dots will blink, meaning they randomly turn on and off, which is quite problematic for single-molecule imaging, and will photobleach, turn-off permanently, usually after less than 10 seconds under most imaging conditions,” Schuck says.

    Five years ago, Cohen and Schuck and their colleagues at the Molecular Foundry synthesized and imaged single UCNPs made from nanocrystals of sodium yttrium fluoride (NaYF4) doped with trace amounts of the lanthanide elements ytterbium, for the sensitizer ions, and erbium, for the emitter ions. These UCNPs were able to upconvert near-infrared photons into green or red visible light, and their photostability makes them potentially ideal luminescent probes for single-molecule imaging.

    “Cells don’t naturally contain lanthanides, so they don’t upconvert light at all, which means we can image without any measurable background,” Cohen says. “And we can excite with near-infrared light, which is a lot less damaging to cells than visible or ultraviolet light. These are great properties, but to make our UCNPs more compatible with cellular imaging, we had to develop new synthetic methods to make them smaller.”

    However, when Foundry scientists shrunk UCNP size, following the conventional design rules, they found that loss of brightness became a major issue. UCNPs smaller than 10 nanometers were no longer bright enough for single molecule imaging. This prompted the new study, which showed that factors known to increase brightness in bulk experiments lose importance at higher excitation powers and that, paradoxically, the brightest probes under single-molecule excitation are barely luminescent at the ensemble level.

    mf
    The Molecular Foundry is one of five DOE Nanoscale Science Research Centers (NSRCs) dedicated to interdisciplinary research at the nanoscale. The Foundry is hosted at Berkeley Lab. (Photo by Roy Kaltschmidt, Berkeley Lab)

    “This discovery came about really as a consequence of the multidisciplinary collaborative environment at the Molecular Foundry,” says Daniel Gargas, co-lead author of the Nature Nanotechnology paper. “By utilizing our daily contact and friendships with scientists throughout the Foundry, we were able to perform highly advanced research on nanoscale materials that included the study of single-molecule photophysics, the ability to synthesize ultra-small upconverting nanocrystals of almost any composition, and the advanced modeling/simulation of UCNP optical properties. There aren’t many facilities in the world that can match this collaborative atmosphere with such high levels of scientific characterization.”

    UCNPs make use of sensitizer ions, such as ytterbium, with relatively large photon absorption cross-sections, to absorb incoming light and transfer this absorbed energy to emitter ions, such as erbium, which luminesce. The original lanthanide-doped UCNPs contained 20-percent ytterbium and 2-percent erbium, which were believed to be the optimal concentrations for brightness in both bulk and nanocrystals. However, the new Molecular Foundry study showed that for UCNPs smaller than 10 nanometers, the erbium concentration could be raised to 20-percent and the ytterbium concentration could be reduced to 2-percent, or even eliminated for UCNPs approaching five nanometers.

    ”People often assume that particles that are the brightest at low powers will also be the brightest at high powers, but we found our ultra-small UCNPs to be a classic tortoise-and-hare example,” says Emory Chan, the other co-lead author of the Nature Nanotechnology paper. “UCNPs heavily doped with erbium start slowly out of the gate, being incredibly dim at low powers, but by the time the laser intensity is cranked up to high power, they have passed up the conventionally doped UCNPs that are the high-flyers at low powers.”

    Chan’s computer models predict that the new rules are universal for lanthanide-doped nanocrystal hosts and he is now using the Foundry’s WANDA robot (Workstation for Automated Nanomaterial Discovery and Analysis), which he developed along with co-author Delia Milliron, to create and screen for the best UCNP compositions based on different operation/application considerations and criteria.

    In the course of discovering the new rules for designing ultra-small UCNPs, the research team also discovered that complex levels of heterogeneity exist within the emission spectra of these UCNPs. This suggests that emissions from the UCNPs may be originating from only a small subset of the total emitters.

    “Future studies may determine how to engineer particles consisting of only these super-emitters resulting in even brighter emissions from ultra-small UCNPs,” Gargas says.

    This research was supported by the DOE Office of Science.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 10:39 am on February 13, 2014 Permalink | Reply
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    From Livermore Lab: “New X-ray analysis method opens the door to researching an elusive class of proteins” 


    Lawrence Livermore National Laboratory

    02/13/2014
    Stephen P Wampler, LLNL, (925) 423-3107, wampler1@llnl.gov

    An international team of researchers has demonstrated a new method for studying the structure of proteins that could lead to important advances in biology and other fields.

    lab
    Beam line scientist Marc Messerschmidt loads a sample holder that supports two-dimensional protein crystals into the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. He co-authored an International Union of Crystallography Journal article on a new method of studying proteins.

    For the first time, protein crystals have been studied in two dimensions at room temperature with X-rays, using a new technique that could open the door for scientists to learn more about an important class of proteins that constitute about one-third of all human proteins. The scientists report their findings about this X-ray diffraction method in the March edition of the International Union of Crystallography Journal.

    “Our work demonstrates for the first time that two-dimensional protein X-ray crystallography is a potential method for obtaining protein structure information,” said Matthias Frank, a physicist at the Department of Energy’s (DOE) Lawrence Livermore National Laboratory (LLNL).

    Frank co-led a team of two dozen scientists with crystallographer James Evans of Pacific Northwest National Laboratory (PNNL) that used the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory in Menlo Park, Calif. The SLAC machine, an X-ray Free Electron Laser (XFEL), is one of two such machines in the world — along with Japan’s SACLA — that can produce hard X-rays.

    Using the predominant method for analyzing protein structures, synchrotron light sources, researchers who take snapshots of proteins must work in three dimensions and need a billion copies of the same protein all stacked up on each other to get a better image of what the protein looks like.

    In effect, synchrotron machines require crystals to be grown in three dimensions to distribute the radiation damage from the X-rays over many molecules, but that makes it difficult to study about one-third of all human proteins, called membrane proteins, because crystals of these proteins are hard to grow in three dimensions.

    Now with the LCLS XFEL machine, scientists can use exceptionally bright and fast X-rays to take a picture that rivals current methods, with a sheet of proteins only one layer thick.

    “We can do this because the X-ray pulses from the LCLS are so bright and so fast that we can produce a measurable X-ray diffraction signal before the sample is destroyed. This type of two-dimensional measurement is not possible at synchrotron light sources because the sample is destroyed by radiation before enough of the signal can be obtained,” Frank said.

    The membrane proteins that can now be studied more easily using the LCLS machine are often embedded in the boundaries of cells and perform a number of vital cell functions, including nutrient uptake, transport and signaling.

    They are important not only because they represent about one-third of all human proteins, but also because they constitute about two-thirds of all current pharmaceutical drug targets for fighting diseases and other human-related health issues.

    “The structures of the proteins tell us about their function, which is why it’s important to better understand their structure,” according to Frank.

    “We believe that ultimately the two-dimensional X-ray crystallography performed at room temperature may someday allow us to observe molecules in action, or to make what some call ‘molecular movies.’ This would permit us to better understand the proteins’ functions and how to control them by drugs,” he continued.

    In 2012, scientists showed they could use an XFEL on a crystal of proteins 10 to 20 sheets thick. Frank, Evans and their team aimed at reducing the number of layers further.

    The team developed a way to create one-sheet-thick layers of two different proteins — a soluble protein called streptravidin that is a commonly used molecule in biology for binding substances and bacteriorhdopsin, a membrane protein isolated from bacteria living in salt ponds. The structures of both proteins are well understood, so the proteins served as model systems.

    The team measured the resolution of the two proteins at 8.5 angstroms (a size that would fit in the period at the end of a sentence more than 500,000 times). In subsequent experiments, they have already obtained better resolutions and eventually, the scientists would like to reach a resolution of 2 angstroms, a level at which individual atoms can be distinguished.

    In addition to Frank, other members of the LLNL multidisciplinary team that assisted in conducting the three-day May 2012 experiments were postdoctoral researcher and physical chemist Mark Hunter, chemist W. Henry Benner, physicist Stefan Hau-Riege, postdoctoral researchers and physicists Tommaso Pardini and Alexander Graf (who has since left LLNL), and biologists Brent Segelke and Matthew Coleman.

    Among the institutions that participated in the research besides LLNL and PNNL were the University of California, Davis, Arizona State University, the Centre for Free Electron Laser Science based in Hamburg, Germany; the Paul Scherrer Institute in Villigen, Switzerland; and the LCLS at the SLAC National Accelerator Laboratory.

    Since 2005, LLNL has conducted proof-of-principle experiments for using X-ray free electron lasers for biological imaging and structural biology. Those experiments were led initially by former LLNL physicist Henry Chapman, who is now a director at the Centre for Free Electron Laser Science in Hamburg.

    The paper is published on the Web in the International Union of Crystallography Journal.

    See the full article here.

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  • richardmitnick 8:31 pm on January 14, 2014 Permalink | Reply
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    From SLAC: “X-ray Laser Maps Important Drug Target” 

    New Technology Allows Faster, More Accurate Imaging of Hard-to-study Membrane Proteins

    December 19, 2013
    No Writer Credit

    Researchers have used one of the brightest X-ray sources on the planet to map the 3-D structure of an important cellular gatekeeper known as a G protein-coupled receptor, or GPCR, in a more natural state than possible before. The new technique is a major advance in exploring GPCRs, a vast, hard-to-study family of proteins that plays a key role in human health and is targeted by an estimated 40 percent of modern medicines.

    The research, performed at the Linac Coherent Light Source (LCLS) X-ray laser at the Department of Energy’s (DOE’s) SLAC National Accelerator Laboratory, is also a leap forward for structural biology experiments at LCLS, which has opened up many new avenues for exploring the molecular world since its launch in 2009.

    migraine
    This illustration shows a man suffering from a migraine, overlain with a rendering of the human serotonin receptor bound to ergotamine, an anti-migraine drug. Also shown is a rendering of a neuron network. Scientists used SLAC’s Linac Coherent Light Source X-ray laser to explore crystallized samples of the serotonin receptor, which is a type of G protein-coupled receptor. GPCRs regulate many important functions in human physiology; serotonin, for example, is a neurotransmitter that regulates mood, appetite and sleep. (Katya Kadyshevskaya/The Scripps Research Institute)

    “For the first time we have a room-temperature, high-resolution structure of one of the most difficult to study but medically important families of membrane proteins,” said Vadim Cherezov, a pioneer in GPCR research at The Scripps Research Institute who led the experiment. “And we have validated this new method so that it can be confidently used for solving new structures.”

    See the full article, with videos, here.

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    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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  • richardmitnick 4:30 pm on November 25, 2013 Permalink | Reply
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    From SLAC: “Scientists Prove X-ray Laser Can Solve Protein Structures from Scratch” 

    November 24, 2013
    Press Office Contact: Andy Freeberg, SLAC National Accelerator Laboratory: afreeberg@slac.stanford.edu, (650) 926-4359

    A study shows for the first time that X-ray lasers can be used to generate a complete 3-D model of a protein without any prior knowledge of its structure.

    protein
    This 3-D rendering of a lysozyme molecule shows two gadolinium atoms bound to it. Researchers soaked lysozyme crystals in a solution containing the metal gadolinium to help improve imaging quality in an experiment at SLAC’s Linac Coherent Light Source X-ray laser. The experiment proved that LCLS can resolve the lysozyme structure without using data obtained earlier, and researchers hope to use similar techniques to reconstruct important unsolved proteins. (Max Planck Society)

    An international team of researchers working at the Department of Energy’s (DOE) SLAC National Accelerator Laboratory produced from scratch an accurate model of lysozyme, a well-studied enzyme found in egg whites, using the Linac Coherent Light Source (LCLS) X-ray laser and sophisticated computer analysis tools.

    lcls
    In crystallography experiments at the Coherent X-ray Imaging experimental station at LCLS, a liquid jet delivers nanoscale crystals into this chamber, where X-ray laser pulses strike them. (Brad Plummer/SLAC)

    The experiment proves that X-ray lasers can play a leading role in studying important biomolecules of unknown structure. The special attributes of LCLS, which allow the study of very small crystals, could cement its role in hunting down many important biological structures that have so far remained out of reach because they form crystals too small for analysis with conventional X-ray sources.

    “Determining protein structures using X-ray lasers requires averaging a gigantic amount of data to get a sufficiently accurate signal, and people wondered if this really could be done,” said Thomas Barends, a staff scientist at the Max Planck Institute for Medical Research in Germany who participated in the research. “Now we have experimental evidence. This really opens the door to new discoveries.”

    Scientist Contacts:
    Thomas Barends, Max Planck Institute for Medical Research: Thomas.Barends@mpimf-heidelberg.mpg.de
    Ilme Schlichting, Max Planck Institute for Medical Research: Ilme.Schlichting@mpimf-heidelberg.mpg.de
    Sebastien Boutet, SLAC National Accelerator Laboratory: sboutet@slac.stanford.edu

    See the full article here.

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    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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  • richardmitnick 8:00 pm on August 29, 2013 Permalink | Reply
    Tags: , , , , Protein Studies   

    From Argonne Lab: “Membrane protein kit may lead to better targeted drugs” 

    News from Argonne National Laboratory

    August 29, 2013
    Chelsea Leu

    Many pharmaceuticals may soon become better targeted and more effective with the help of new technology developed at the U.S. Department of Energy’s Argonne National Laboratory.

    This technology, the Rhodobacter Membrane Protein Expression System, received one of this year’s R&D 100 Awards. These prestigious awards, known as “the Oscars of Innovation,” recognize the most important scientific and technological breakthroughs of the year. The winning invention, developed by Argonne biologists Philip Laible and Deborah Hanson, enables its users to easily generate large amounts of membrane proteins.

    tweo
    Argonne biologists Deborah Hanson and Phil Laible developed a kit that enables its users to easily generate large amounts of membrane proteins.

    Membrane proteins are proteins embedded into the surfaces of cells that carry out vital processes necessary to the cells’ survival. They act as gatekeepers, controlling which drugs can access the cell. These proteins can make or break a drug, and are so important in disease that more than half of all new drugs in development target membrane proteins.

    For researchers to design better targeted drugs, they need to know the structure and functional characteristics of these membrane proteins. Determining these characteristics is difficult, because researchers need large amounts of membrane protein to characterize their functions and map their structures, and sources are scarce.

    Few prior technologies were able to produce membrane proteins in large amounts, in part because membrane proteins are finicky and difficult to work with. They cannot function in water, so the proteins must be protected by a layer of membrane almost immediately after they are generated inside the cell. Otherwise, they will degrade from exposure to an incompatible environment.

    Laible and Hanson sought to change this. With their new kit, membrane proteins can be produced in unprecedented quantities. “This kit is the first of its kind to be designed specifically for the production of membrane proteins,” Hanson said.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus


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  • richardmitnick 10:33 am on August 8, 2013 Permalink | Reply
    Tags: , , , , Protein Studies,   

    From SLAC: “New Analysis Shows How Proteins Shift Into Working Mode” 

    August 8, 2013
    Mike Ross

    “In an advance that will help scientists design and engineer proteins, a team including researchers from SLAC and Stanford has found a way to identify how protein molecules flex into specific atomic arrangements required to catalyze chemical reactions essential for life.

    The achievement, published Sunday (Aug. 4, 2013) in Nature Methods, uses a new computer algorithm to analyze data from X-ray studies of crystallized proteins. Scientists were able to identify cascades of atomic adjustments that shift protein molecules into new shapes, or conformations.

    prot
    This 3-D figure of the enzyme dihydrofolate reductase (dhfr) shows the nine different areas where a small fluctuation in one part of this flexible molecule causes a sequence of atomic movements to propagate like falling dominoes. A new computer algorithm, CONTACT, identified these areas, which are colored red, yellow, green, orange, salmon, grey, light blue, dark blue and purple.

    ‘Proteins need to move around to do their part in keeping the organism alive,’ said Henry van den Bedem, first author on the paper and a researcher with the Structure Determination Core of the Joint Center for Structural Genomics (JCSG) at the SSRL Directorate of SLAC. ‘But often these movements are very subtle and difficult to discern. Our research is aimed at identifying those fluctuations from X-ray data and linking them to a protein’s biological functions. Our work provides important new insights, which will eventually allow us to re-engineer these molecular machines.'”

    hb
    Henry van den Bedem. (Matt Beardsley/SLAC)

    Central to the new technique is a new computer algorithm, called CONTACT, that analyzes protein structures determined by room temperature X-ray crystallography. Built upon an earlier algorithm created by van den Bedem, CONTACT detects how subtle features in the experimental data produced by changing conformations propagate through the protein and identifies regions within the protein where these cascades of small changes are likely to result in stable conformations.

    The research team also included scientists from University of California-San Francisco and The Scripps Research Institute in La Jolla.

    See the full article here.

    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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  • richardmitnick 3:02 pm on April 29, 2013 Permalink | Reply
    Tags: , , , Protein Studies   

    From Berkeley Lab: “Comparing Proteins at a Glance” 


    Berkeley Lab

    Berkeley Lab Researchers Unveil Technique for Easy Comparisons of Proteins in Solution

    April 29, 2013
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    “A revolutionary X-ray analytical technique that enables researchers at a glance to identify structural similarities and differences between multiple proteins under a variety of conditions has been developed by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). As a demonstration, the researchers used this technique to gain valuable new insight into a protein that is a prime target for cancer chemotherapy.

    map
    Data in this revolutionary structural comparison map is presented as a color-coded checkerboard with similarity scores displayed as gradients moving from red, indicating high, to white, indicating low, and various shades of orange and yellow in between. No image credit

    ‘Proteins and other biological macromolecules are moving machines whose power is often derived from how their structural conformations change in response to their environment,’ says Greg Hura, a scientist with Berkeley Lab’s Physical Biosciences Division. ‘Knowing what makes a protein change has incredible value, much like knowing that stepping on a gas pedal makes the wheels of a car spin.’

    Hura led the development of what is being called a structural comparison map for use with small angle X-ray scattering
    (SAXS), an imaging technique for obtaining structural information about proteins and protein complexes in solution. Cynthia McMurray, a biologist with Berkeley Lab’s Life Sciences Division, provided the cancer-relevant protein used to test the new SAXS structural comparison map.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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    DOE Seal


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