Tagged: SLAC LCLS Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 10:24 pm on September 20, 2017 Permalink | Reply
    Tags: , , , SLAC LCLS,   

    From SLAC: “High-Speed Movie Aids Scientists Who Design Glowing Molecules” 


    SLAC Lab

    September 20, 2017
    Amanda Solliday

    1
    Aequorea victoria, also called the crystal jelly, is a bioluminescent jellyfish that lives near the Pacific coast of North America. (Gary Kavanagh/iStockphoto.com)

    2
    The Coherent X-Ray Imaging (CXI) instrument makes use of the brilliant hard X-ray pulses from the Linac Coherent Light Source. The equipment is tailored for X-ray crystallography experiments. (SLAC National Accelerator Laboratory)

    SLAC/LCLS

    With SLAC’s X-ray laser, a research team captured ultrafast changes in fluorescent proteins between “dark” and “light” states. The insights allowed the scientists to design improved markers for biological imaging.

    The crystal jellyfish swims off the coast of the Pacific Northwest and can illuminate the waters when disturbed. That glow comes from proteins that absorb energy and then release it as bright flashes.

    To track many of life’s activities, biologists took a cue from this same jellyfish.

    Scientists collected one of the proteins found in the sea creatures, green fluorescent protein (GFP), and engineered a molecular light switch that would glow or remain dark depending on specific experimental conditions. The glowing labels are attached to molecules in living cells so researchers can highlight them during imaging experiments. They use these fluorescent markers to understand how a cell responds to changes in its environment, identify which molecules interact within a cell and track the effects of genetic mutations.

    Researchers have studied GFP and other fluorescent proteins for decades to better understand their glowing action and improve their function in scientific studies, but they have never been able to observe the ultrafast changes that occur between “off” and “on” states until now.

    In a recent experiment conducted at the Department of Energy’s SLAC National Accelerator Laboratory, a research team used bright, ultrafast X-ray pulses from SLAC’s X-ray free-electron laser to create a high-speed movie of a fluorescent protein in action. With that information, the scientists began to design a marker that switches more easily, a quality that can improve resolution during biological imaging.

    “We think that this approach will open a world of possibilities to tailor fluorescent proteins,” says Martin Weik, scientist at the Institute of Structural Biology in Grenoble, France and one of the authors on the publication. “We not only have the structure of the fluorescent protein, but now we can see what is happening between one static state and the other.”

    Nature Chemistry published the study on Sept. 11.

    Filming a Molecular Light Switch

    To observe these intermediate states, the scientists initiated a photochemical reaction in the fluorescent protein with an optical laser at the Coherent X-ray Imaging instrument at the Linac Coherent Light Source, followed by X-ray snapshots at distinct time delays. The optical laser provides energy in the form of photons, mimicking what happens in nature.

    “Atoms move around in the photoactive site of the molecule as a result of absorption of a photon,” says Sebastien Boutet, SLAC scientist and a co-author of the paper. “This structural change turns the protein from a dark state to a light-emitting (fluorescent) state.”

    There’s a vast body of literature calculating what might happen between the two states, but no one studying the protein was able to see the structural changes in the switch as the photon is absorbed. The molecular switch was just too fast for traditional X-ray imaging techniques.

    In this study, the femtosecond X-ray pulses generated by LCLS—arriving in just millionths of a billionth of a second—allowed the team to create stop-action images of the process at an extremely close interval after the proteins were activated by the optical laser.

    A Door Half Open

    The high-speed snapshots were used to generate a movie starting from the dark state, and gave the researchers insights that they used to design more efficient switchable light-emitting proteins. They found a clue in the time the molecules spent between fluorescent and non-fluorescent states.

    “After a picosecond, and for a very short time, this molecular switch is stuck between on and off,” says Ilme Schlichting, scientist at the Max-Planck Institute in Heidelberg, Germany and one of the authors on the publication. “People have predicted this, but to actually visualize its structure is extremely exciting.”

    “It’s as if there’s a door and it’s neither closed nor completely open; it’s half open,” she says. “And now we are learning what can go through the door, what might be blocking it and how it works in real time.”

    In this study, the scientists found that an amino acid blocked the door and prevented the switch from flipping as easily as possible.

    The researchers shortened the amino acid in a mutated version of the fluorescent protein. This engineered version switched more easily and gave better contrast. These traits will allow scientists to observe cellular activity with greater precision.

    “Contrast is essential in imaging. It’s like on a TV screen, where to see the best picture, you want the dark to be extremely dark and the color to be super bright and colorful,” says Jacques-Philippe Colletier, a scientist at the Institute of Structural Biology who contributed to the research.

    This new molecular movie featuring the jellyfish-inspired proteins lights the way to capture more of life’s microscopic details. The team will continue to fine-tune the protein for other desired characteristics that make it ideal for “super-resolution microscopy,” a type of light microscopy where scientists are able to see illuminated details of cells not distinguishable with conventional light microscopy methods.

    The research collaboration included several French institutions, including the Institute of Structural Biology, University of Lille, University of Paris-Sud and the University of Rennes, as well as Max Planck Institutes in Germany and SLAC.

    LCLS is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

    Advertisements
     
  • richardmitnick 7:35 am on September 1, 2017 Permalink | Reply
    Tags: , , , , MEC- Matter in Extreme Conditions, , SLAC LCLS, ,   

    From SLAC: “Newly Upgraded Laser Allows Scientists to Peer Further Into the Extreme Universe at SLAC’s LCLS” 


    SLAC Lab

    August 15, 2017
    Miyuki Dougherty

    1
    Highly reflective mirrors and telescope lenses in the Matter in Extreme Conditions (MEC) optical laser system are carefully positioned to propagate the instrument’s high-quality laser beams. The laser beams create extreme pressure and temperature conditions in materials that are instantaneously probed using hard X-rays from SLAC’s Linac Coherent Light Source (LCLS). (Dawn Harmer/SLAC National Accelerator Laboratory)

    Tripling the energy and refining the shape of optical laser pulses at the Matter in Extreme Conditions instrument allows researchers to create higher-pressure conditions and explore unsolved fusion energy, plasma physics and materials science questions.

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory recently upgraded a powerful optical laser system used to create shockwaves that generate high-pressure conditions like those found within planetary interiors. The laser system now delivers three times more energy for experiments with SLAC’s ultrabright X-ray laser, providing a more powerful tool for probing extreme states of matter in our universe.

    Together, the optical and X-ray lasers form the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS).

    SLAC/LCLS

    The high-power optical laser system creates extreme temperature and pressure conditions in materials, and the X-ray laser beam captures the material’s response.

    With this technology, researchers have already examined how meteor impacts shock minerals in the Earth’s crust and simulated conditions in Jupiter’s interior by turning aluminum foil into a warm, dense plasma.

    Higher Intensity and More Controlled Pulse Shapes

    The MEC instrument team received funding from the Office of Fusion Energy Sciences (FES) within the DOE’s Office of Science to double the amount of energy the optical beam can deliver in 10 nanoseconds, from 20 to 40 joules.

    But they went even further.

    “The team exceeded our expectations, an exciting accomplishment for the DOE High Energy Density program and future MEC instrument users,” says Kramer Akli, program manager for High Energy Density Laboratory Plasma at FES.

    The team tripled the amount of energy the laser can deliver in 10 nanoseconds to a spot on a target no bigger than the width of a few human hairs. When focused down to that small area, the laser provides users with intensities up to 75 terawatts per square centimeter.

    “In other terms, the upgraded laser has the same power as 17 Teslas discharging their 100 kilowatt-hour batteries in one second,” says Eric Galtier, a MEC instrument scientist.

    A portion of the energy upgrade can be attributed to the optical laser’s new, homemade diode pumped front-end, designed with the help of Marc Welch, a MEC laser engineer. The scientists also built and automated a system for shaping the laser pulses with extraordinary precision, allowing users substantially greater flexibility and control over the pulse shapes used in their experiments.

    A more powerful and reliable laser means that researchers can study higher pressure regimes and reach conditions relevant to fusion energy studies.

    Simulating the Core of Planets

    The MEC upgrade is promising for many researchers, including Shaughnessy Brennan Brown, a doctoral student in Mechanical Engineering, whose research focuses on high energy density science, which spans chemistry, materials science, and physics. Brennan Brown uses the MEC experimental hutch to drive shock waves through silicon and generate high-pressure conditions that occur in the Earth’s interior.

    “The MEC upgrade at LCLS enables researchers like me to generate exciting, previously-unexplored regimes of exotic matter – such as those found on Mars, our next planetary stepping stone – with crucial reliability and repeatability,” Brennan Brown says.

    Brennan Brown’s research examines the processes by which silicon in Earth’s core rearranges atomically under high temperature and pressure conditions. The thermodynamic properties of these high-pressure states affect our magnetic field, which protects us from the solar wind and allows us to survive on Earth. The laser upgrade will permit Brennan Brown to reach higher pressure and temperature conditions inside her samples, a long-standing goal.

    2
    Inside the MEC vacuum target chamber where researchers create transient states of matter using high-power optical lasers, which are then examined with SLAC’s Linac Coherent Light Source (LCLS) X-rays. (Matt Beardsley/SLAC National Accelerator Laboratory)

    Intensity Plus Precision

    The optical laser amplifies a low-power beam in stages and reaches increasingly high energies. However, the quality of the laser beam and ability to control it diminish during amplification. A low-quality pulse may start and end with a significantly different shape, which is not useful for researchers trying to recreate specific conditions.

    “The initial low energy pulse must have a pristine spatial mode and the properly configured temporal shape – that is, a precise sculpting of the pulse’s power as a function of time – before amplification to produce the laser pulse characteristics needed to enable each users’ experiment,” says Michael Greenberg, the MEC Laser Area Manager.

    Each target is unique and requires a specific energy and pulse shape, making manual tests and adjustments time-consuming. Prior to the upgrade, the team optimized the pulse shape by hand, taking anywhere from a few hours to a few days to properly calibrate it.

    To resolve this issue, Eric Cunningham, a laser scientist at MEC, developed an automated control system to shape the low-powered beam before amplification.

    3
    To demonstrate the MEC laser system’s enhanced ability to tailor the shape of laser pulses, scientists generated pulse shapes that spell out “M-E-C” in a plot of laser intensity vs. time. (Eric Cunningham and Michael Greenberg/SLAC National Accelerator Laboratory)

    “The new system allows for precise tailoring of the pulse shape using a computerized feedback loop system that analyzes the pulses and automatically re-calibrates the laser,” Cunningham said. The new optimizer is a promising system for generating many high-quality pulses in the most accurate and timely manner possible.

    In addition to the improved pulse shapes, the upgraded system deposits energy on samples more consistently from shot to shot, which allows researchers to very closely reproduce extreme states of matter in their samples. As a result, both the data quality and operational efficiency are improved.

    Brennan Brown says it’s the people and technology that make the instrument so successful: “The capability and competency of the laser scientists and engineers at the MEC experimental station offer researchers the technological resources they need to explore unanswered questions of the universe and bring their theories to life.”

    LCLS is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 10:56 am on August 21, 2017 Permalink | Reply
    Tags: , Diamond rain, MEC-Matter in Extreme Conditions instrument, , SLAC LCLS,   

    From SLAC: “Scientists Create ‘Diamond Rain’ That Forms in the Interior of Icy Giant Planets” 


    SLAC Lab

    August 21, 2017
    Amanda Solliday
    solliday@slac.stanford.edu
    (650) 926-4496

    1
    A cutaway depicts the interior of Neptune (left). In an experiment conducted at the Linac Coherent Light Source, the team studied a plastic simulating compounds formed from methane—a molecule with just one carbon bound to four hydrogen atoms that causes the distinct blue cast of Neptune. Methane forms hydrocarbon (hydrogen and carbon) chains that respond to high pressure and temperature to form “diamond rain” in the interiors of icy giant planets like Neptune. The scientists were able to recreate similar conditions using high-powered optical lasers and watch the small diamonds form in real time with X-rays. (Greg Stewart/SLAC National Accelerator Laboratory)

    In an experiment designed to mimic the conditions deep inside the icy giant planets of our solar system, scientists were able to observe “diamond rain” for the first time as it formed in high-pressure conditions. Extremely high pressure squeezes hydrogen and carbon found in the interior of these planets to form solid diamonds that sink slowly down further into the interior.

    The glittering precipitation has long been hypothesized to arise more than 5,000 miles below the surface of Uranus and Neptune, created from commonly found mixtures of just hydrogen and carbon. The interiors of these planets are similar—both contain solid cores surrounded by a dense slush of different ices. With the icy planets in our solar system, “ice” refers to hydrogen molecules connected to lighter elements, such as carbon, oxygen and/or nitrogen.

    Researchers simulated the environment found inside these planets by creating shock waves in plastic with an intense optical laser at the Matter in Extreme Conditions (MEC) instrument at SLAC National Accelerator Laboratory’s X-ray free-electron laser, the Linac Coherent Light Source (LCLS).

    SLAC/LCLS

    SLAC is one of 10 Department of Energy (DOE) Office of Science laboratories.

    In the experiment, the scientists were able to see that nearly every carbon atom of the original plastic was incorporated into small diamond structures up to a few nanometers wide. On Uranus and Neptune, the study authors predict that diamonds would become much larger, maybe millions of carats in weight. Researchers also think it’s possible that over thousands of years, the diamonds slowly sink through the planets’ ice layers and assemble into a thick layer around the core.

    The research published in Nature Astronomy on August 21.

    “Previously, researchers could only assume that the diamonds had formed,” said Dominik Kraus, scientist at Helmholtz Zentrum Dresden-Rossendorf and lead author on the publication. “When I saw the results of this latest experiment, it was one of the best moments of my scientific career.”

    Earlier experiments that attempted to recreate diamond rain in similar conditions were not able to capture measurements in real time, because we currently can create these extreme conditions under which tiny diamonds form only for very brief time in the laboratory. The high-energy optical lasers at MEC combined with LCLS’s X-ray pulses—which last just femtoseconds, or quadrillionths of a second—allowed the scientists to directly measure the chemical reaction.

    Other prior experiments also saw hints of carbon forming graphite or diamond at lower pressures than the ones created in this experiment, but with other materials introduced and altering the reactions.

    The results presented in this experiment is the first unambiguous observation of high-pressure diamond formation from mixtures and agrees with theoretical predictions about the conditions under which such precipitation can form and will provide scientists with better information to describe and classify other worlds.

    Turning Plastic Into Diamond

    In the experiment, plastic simulates compounds formed from methane—a molecule with just one carbon bound to four hydrogen atoms that causes the distinct blue cast of Neptune.

    The team studied a plastic material, polystyrene, that is made from a mixture of hydrogen and carbon, key components of these planets’ overall chemical makeup.

    In the intermediate layers of icy giant planets, methane forms hydrocarbon (hydrogen and carbon) chains that were long hypothesized to respond to high pressure and temperature in deeper layers and form diamond rain.

    The researchers used high-powered optical laser to create pairs of shock waves in the plastic with the correct combination of temperature and pressure. The first shock is smaller and slower and overtaken by the stronger second shock. When the shock waves overlap, that’s the moment the pressure peaks and when most of the diamonds form, Kraus said.

    During those moments, the team probed the reaction with pulses of X-rays from LCLS that last just 50 femtoseconds. This allowed them to see the small diamonds that form in fractions of a second with a technique called femtosecond X-ray diffraction. The X-ray snapshots provide information about the size of the diamonds and the details of the chemical reaction as it occurs.

    “For this experiment, we had LCLS, the brightest X-ray source in the world,” said Siegfried Glenzer, professor of photon science at SLAC and a co-author of the paper. “You need these intense, fast pulses of X-rays to unambiguously see the structure of these diamonds, because they are only formed in the laboratory for such a very short time.”

    2
    The Matter in Extreme Conditions instrument at SLAC gives scientists the tools to investigate the extremely hot, dense matter at the centers of stars and giant planets. These experiments could help researchers design new materials with enhanced properties and recreate the nuclear fusion process that powers the sun. (SLAC National Accelerator Laboratory)

    Nanodiamonds at Work

    When astronomers observe exoplanets outside our solar system, they are able to measure two primary traits—the mass, which is measured by the wobble of stars, and radius, observed from the shadow when the planet passes in front of a star. The relationship between the two is used to classify a planet and help determine whether it may be composed of heavier or lighter elements.

    “With planets, the relationship between mass and radius can tell scientists quite a bit about the chemistry,” Kraus said. “And the chemistry that happens in the interior can provide additional information about some of the defining features of the planet.”

    Information from studies like this one about how elements mix and clump together under pressure in the interior of a given planet can change the way scientists calculate the relationship between mass and radius, allowing scientists to better model and classify individual planets. The falling diamond rain also could be an additional source of energy, generating heat while sinking towards the core.

    “We can’t go inside the planets and look at them, so these laboratory experiments complement satellite and telescope observations,” Kraus said.

    The researchers also plan to apply the same methods to look at other processes that occur in the interiors of planets.

    In addition to the insights they give into planetary science, nanodiamonds made on Earth could potentially be harvested for commercial purposes—uses that span medicine, scientific equipment and electronics. Currently, nanodiamonds are commercially produced from explosives; laser production may offer a cleaner and more easily controlled method.

    Research that compresses matter, like this study, also helps scientists understand and improve fusion experiments where forms of hydrogen combine to form helium to generate vast amounts of energy. This is the process that fuels the sun and other stars but has yet to be realized in a controlled way for power plants on Earth.

    In some fusion experiments, a fuel of two different forms of hydrogen is surrounded by a plastic layer that reaches conditions similar to the interior of planets during a short-lived compression stage. The LCLS experiment on plastic now suggests that chemistry may play an important role in this stage.

    “Simulations don’t really capture what we’re observing in this field,” Glenzer said. “Our study and others provide evidence that matter clumping in these types of high-pressure conditions is a force to be reckoned with.”

    The research collaboration includes scientists from Helmholtz Zentrum Dresden-Rossendorf in Germany, University of California-Berkeley, Lawrence Livermore National Laboratory, Lawrence Berkeley National Laboratory, GSI Helmholtz Center for Heavy Ion Research in Germany, Osaka University in Japan, Technical University of Darmstadt in Germany, European XFEL, University of Michigan, University of Warwick in the United Kingdom and SLAC.

    The research was supported by DOE’s Office of Science and the National Nuclear Security Administration. LCLS is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 12:58 pm on July 19, 2017 Permalink | Reply
    Tags: , , New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers, , SLAC LCLS,   

    From SLAC: “New Droplet-on-Tape Method Assists Biochemical Research at X-Ray Lasers” 


    SLAC Lab

    February 27, 2017 [Never saw this one before]

    1
    Acoustic droplet ejection allows scientists to deposit nanoliters of sample directly into the X-ray beam, considerably increasing the efficiency of sample consumption. A femtosecond pulse from an X-ray free-electron laser then intersects with a droplet that contains protein crystals. (SLAC National Accelerator Laboratory)

    SLAC/LCLS

    2
    As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. (SLAC National Accelerator Laboratory)

    Biological samples studied with intense X-rays at free-electron lasers are destroyed within nanoseconds after they are exposed. Because of this, the samples need to be continually refreshed to allow the many images needed for an experiment to be obtained. Conventional methods use jets that supply a continuous stream of samples, but this can be very wasteful as the X-rays only interact with a tiny fraction of the injected material.

    To help address this issue, scientists at the Department of Energy’s Lawrence Berkeley National Laboratory, SLAC National Accelerator Laboratory, Brookhaven National Laboratory, and other institutes designed a new assembly-line system that rapidly replaces exposed samples by moving droplets along a miniature conveyor belt, timed to coincide with the arrival of the X-ray pulses.

    The droplet-on-tape system now allows the team to study the biochemical reactions in real-time from microseconds to seconds, revealing the stages of these complex reactions.

    In their approach, protein solution or crystals are precisely deposited in tiny liquid drops, made as ultrasound waves push the liquid onto a moving tape. As the drops move forward, they are hit with pulses of visible light or treated with oxygen gas, which triggers different chemical reactions depending on the sample studied. This allows the study of processes such as photosynthesis, which determines how plants absorb light from the sun and convert it into useable energy.

    Finally, powerful X-ray pulses from SLAC’s X-ray laser, the Linac Coherent Light Source (LCLS), probe the drops. In this study published in Nature Methods, the X-ray light scattered from the sample onto two different detectors simultaneously, one for X-ray crystallography and the other for X-ray emission spectroscopy. These are two complementary methods that provide information about the geometric and electronic structure of the catalytic sites of the proteins and allowed them to watch with atomic precision how the protein structures changed during the reaction.

    Below, see the conveyor belt in action at LCLS, a Department of Energy Office of Science User Facility.

    3
    Droplet-on-tape conveyor belt system delivers samples at the Linac Coherent Light Source (LCLS). (SLAC National Accelerator Laboratory)

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 9:24 am on July 13, 2017 Permalink | Reply
    Tags: , extraterrestrial ice can form in just billionths of a second, , , SLAC LCLS, Stanford scientists discover how dense, ,   

    From Stanford: “Stanford scientists discover how dense, extraterrestrial ice can form in just billionths of a second” 

    Stanford University Name
    Stanford University

    July 12, 2017
    Adam Hadhazy

    1
    At the Linac Coherent Light Source, Stanford scientists used the world’s most powerful X-ray laser to create an extraterrestrial form of ice. (Image credit: Brad Plummer).

    Stanford researchers have for the first time captured the freezing of water, molecule-by-molecule, into a strange, dense form called ice VII (“ice seven”), found naturally in otherworldly environments, such as when icy planetary bodies collide.

    In addition to helping scientists better understand those remote worlds, the findings – published online July 11 in Physical Review Letters – could reveal how water and other substances undergo transitions from liquids to solids. Learning to manipulate those transitions might open the way someday to engineering materials with exotic new properties.

    “These experiments with water are the first of their kind, allowing us to witness a fundamental disorder-to-order transition in one of the most abundant molecules in the universe,” said study lead author Arianna Gleason, a postdoctoral fellow at Los Alamos National Laboratory and a visiting scientist in the Extreme Environments Laboratory of Stanford’s School of Earth, Energy & Environmental Sciences.

    Scientists have long studied how materials undergo phase changes between gas, liquid and solid states. Phase changes can happen rapidly, however, and on the tiny scale of mere atoms. Previous research has struggled to capture the moment-to-moment action of phase transitions, and instead worked backward from stable solids in piecing together the molecular steps taken by predecessor liquids.

    “There have been a tremendous number of studies on ice because everyone wants to understand its behavior,” said study senior author Wendy Mao, an associate professor of geological sciences and a Stanford Institute for Materials and Energy Sciences (SIMES) principal investigator. “What our new study demonstrates, and which hasn’t been done before, is the ability to see the ice structure form in real time.”

    Catching ice in the act

    Those timescales became achievable thanks to the Linac Coherent Light Source, the world’s most powerful X-ray laser located at the nearby SLAC National Accelerator Laboratory. There, the science team beamed an intense, green-colored laser at a small target containing a sample of liquid water. The laser instantly vaporized layers of diamond on one side of the target, generating a rocket-like force that compressed the water to pressures exceeding 50,000 times that of Earth’s atmosphere at sea level.

    As the water compacted, a separate beam from an instrument called the X-ray Free Electron Laser arrived in a series of bright pulses only a femtosecond, or a quadrillionth of a second, long. Akin to camera flashes, this strobing X-ray laser snapped a set of images revealing the progression of molecular changes, flip book–style, while the pressurized water crystallized into ice VII. The phase change took just 6 billionths of a second, or nanoseconds. Surprisingly, during this process, the water molecules bonded into rod shapes, and not spheres as theory predicted.

    The platform developed for this study – combining high pressure with snapshot images – could help researchers probe the myriad ways water freezes, depending on pressure and temperature. Under the conditions on our planet’s surface, water crystallizes in only one way, dubbed ice Ih (“ice one-H”) or simply “hexagonal ice,” whether in glaciers or ice cube trays in the freezer.

    Delving into extraterrestrial ice types, including ice VII, will help scientists model such remote environments as comet impacts, the internal structures of potentially life-supporting, water-filled moons like Jupiter’s Europa, and the dynamics of jumbo, rocky, oceanic exoplanets called super-Earths.

    “Any icy satellite or planetary interior is intimately connected to the object’s surface,” Gleason said. “Learning about these icy interiors will help us understand how the worlds in our solar system formed and how at least one of them, so far as we know, came to have all the necessary characteristics for life.”

    Other co-authors on the study include Cindy Bolme of Los Alamos National Laboratory; Eric Galtier, Hae Ja Lee and Eduardo Granados of the SLAC National Accelerator Laboratory; Dan Dolan, Chris Seagle and Tom Ao of Sandia National Laboratories; and Suzanne Ali, Amy Lazicki, Damian Swift and Peter Celliers of Lawrence Livermore National Laboratory.

    Funding was provided by the National Science Foundation, the Los Alamos National Laboratory, the U.S. Department of Energy Office of Science, Fusion Energy Science and the SLAC National Accelerator Laboratory.

    See the full article here .

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

    Stanford University Seal

     
  • richardmitnick 8:17 am on July 7, 2017 Permalink | Reply
    Tags: , , , , , Scientists Get First Direct Look at How Electrons ‘Dance’ with Vibrating Atoms, SLAC LCLS   

    From SLAC: “Scientists Get First Direct Look at How Electrons ‘Dance’ with Vibrating Atoms” 


    SLAC Lab

    July 6, 2017
    No writer credit

    A precise new way to study materials shows this ‘electron-phonon coupling’ can be far stronger than predicted, and could potentially play a role in unconventional superconductivity.

    1
    In this illustration, an infrared laser beam (orange) triggers atomic vibrations in a thin layer of iron selenide, which are then recorded by ultrafast X-ray laser pulses (white) to create an ultrafast movie. The motion of the selenium atoms (red) changes the energy of the electron orbitals of the iron atoms (blue), and the resulting electron vibrations are recorded separately with a technique called ARPES (not shown). The coupling of atomic positions and electronic energies is much stronger than previously thought and may significantly impact the material’s superconductivity. (Greg Stewart/SLAC National Accelerator Laboratory)

    Scientists at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University have made the first direct measurements, and by far the most precise ones, of how electrons move in sync with atomic vibrations rippling through an exotic material, as if they were dancing to the same beat.

    The vibrations are called phonons, and the electron-phonon coupling the researchers measured was 10 times stronger than theory had predicted – making it strong enough to potentially play a role in unconventional superconductivity, which allows materials to conduct electricity with no loss at unexpectedly high temperatures.

    What’s more, the approach they developed gives scientists a completely new and direct way to study a wide range of “emergent” materials whose surprising properties emerge from the collective behavior of fundamental particles, such as electrons. The new approach investigates these materials through experiments alone, rather than relying on assumptions based on theory.

    The experiments were carried out with SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser and with a technique called angle-resolved photoemission spectroscopy (ARPES) on the Stanford campus. The researchers described the study today in Science.

    SLAC/LCLS

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 8:22 am on June 23, 2017 Permalink | Reply
    Tags: , , , How a Single Chemical Bond Balances Cells Between Life and Death, Protein cytochrome c, SLAC LCLS, , ,   

    From SLAC: “How a Single Chemical Bond Balances Cells Between Life and Death” 


    SLAC Lab

    June 22, 2017
    Amanda Solliday

    1
    An optical laser (green) excites the iron-containing active site of the protein cytochrome c, and then an X-ray laser (white) probes the iron a few femtoseconds to picoseconds later. The critical iron-sulfur bond is broken as the optical laser heats the protein, and rebinds as the system cools. (Greg Stewart/SLAC National Accelerator Laboratory)

    Slight changes in the machinery of a cell determine whether it lives or begins a natural process known as programmed cell death. In many forms of life—from bacteria to humans—a single chemical bond in a protein called cytochrome c can make this call. As long as the bond is intact, the protein transfers electrons needed to produce energy through respiration. When the bond breaks, the protein switches gear and triggers the breakdown of mitochondria, the structures that power the cell’s activities.

    For the first time, scientists have measured exactly how much energy cytochrome c puts into maintaining that bond in a state where it’s strong enough to endure, but easy enough to break when the cell’s life span is ending.

    They used intense X-rays from two facilities, the Linac Coherent Light Source (LCLS) X-ray free-electron laser and the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory.

    SLAC/LCLS

    SLAC/SSRL

    The collaboration, led by Edward Solomon, professor of chemistry at Stanford University and of photon science at SLAC, published their results today in Science.

    “This is a very general yet extremely important process in biochemistry, and with an X-ray laser we now have insight into how this regulation works,” says Roberto Alonso-Mori, LCLS staff scientist and a co-author of the study. “These are processes that are going on a million-fold in our bodies and everywhere there is life.”

    The study marks the first time that anyone has been able to experimentally quantify how the rigid structure of the cytochrome c molecule supports this crucial bond between iron and sulfur atoms in what’s known as an entatic state, where the protein maintains a bond that is just strong enough to perform both of its jobs, says Michael Mara, lead author of the study and a former postdoctoral researcher at Stanford University, now at University of California, Berkeley.

    “This was important because we had shown the bond is weak and shouldn’t be present at room temperature in the absence of the protein constraints,” says Solomon. “But the protein is able to contribute energy to keep this bond intact for electron transfer. In this LCLS experiment, we determined exactly how much energy the rest of the protein contributes to maintaining the bond: about 4 kcal/mol that is derived from an adjacent hydrogen bond network.”

    “We were able to show how nature tunes this system to change the properties on a fundamental level and perform two very different functions,” Mara says. “The energy contribution by cytochrome c is really at a sweet spot. It makes me wonder what sort of similar effects you might see in other protein systems, and it makes us realize that there is exciting new science on the horizon.”

    Ultrafast Changes

    Cytochrome c is present in a wide range of life forms and contributes to both cellular respiration and programmed cell death, the pathway to the natural end of a cell’s life cycle. How exactly the state of the bond relates to these two functions had not yet been demonstrated or quantified.

    Scientists knew from earlier studies that a particular iron-sulfur bond is key. When iron in the protein binds to sulfur contained in one of the protein’s amino-acid building blocks, cytochrome c participates in electron transfer. By transferring electrons, the protein helps generate energy needed for biological processes that maintain life.

    But when cytochrome c encounters cardiolipin, a lipid present in the membrane of the cell’s mitochondria, the iron-sulfur bond breaks, and the protein becomes an enzyme that creates holes in the mitochondria’s outer membrane – the first step in programmed cell death.

    These changes occur incredibly fast, in less than 20 picoseconds, so the experiment required ultrafast pulses of X-rays generated by LCLS to take snapshots of the process.

    “We photoexcited the iron atoms in the protein’s active site—which contains an iron-rich compound known as heme—with an ultrafast laser before probing it with the LCLS X-ray pulses at different time delays,” says Alonso-Mori.

    Each 50-femtosecond laser pulse heated the heme by a couple of hundred degrees. X-ray pulses from LCLS took images of what happened as the heat traveled from the iron to other parts of the protein. After 100 femtoseconds, the iron-sulfur bond would break, only to form again once the sample cooled. Watching this process allowed the scientists to measure energy fluctuations in real time and better understand how this critical bond forms and breaks.

    “The entatic state concept is really interesting, but you have to come up with creative ways to demonstrate and quantify it,” says Ryan Hadt, a former Stanford University doctoral student on an Enrico Fermi Fellowship at Argonne National Laboratory who together with his advisor, Professor Solomon, came up with the idea for the experiment and co-wrote the initial proposal around the time LCLS first came online in 2009.

    “Our research group was excited about this new instrument and wanted to use it to do a definitive experiment,” Hadt adds.

    A Question Raised by Earlier Work

    This experiment builds on an earlier study [JACS] conducted at SSRL that found that the iron-sulfur bond was quite weak, says Thomas Kroll, staff scientist at SSRL and lead author of this prior study.

    In the latest study, spectroscopy at SSRL also built the framework for the LCLS pump-probe experiment. It allowed the scientists to compare what the molecule originally looked like to how it changed when the temperature rose.

    “It’s important to understand how these proteins actually work,” Kroll says. “Because if you don’t understand how they work, how can we create better medicines in an informed and controlled way?”

    Knowledge of cytochrome c’s function is also valuable to the fields of bioenergy and environmental science, since it is a critically important protein in bacteria and plants.

    The DOE Office of Science and the National Institute of General Medical Sciences of the National Institutes of Health supported this research. The Structural Molecular Biology program at SSRL is funded by DOE Office of Science and the National Institutes of Health, National Institute of General Medical Sciences. LCLS and SSRL are DOE Office of Science User Facilities.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 8:06 am on June 23, 2017 Permalink | Reply
    Tags: A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response, , , , , , SLAC LCLS,   

    From SLAC: “A Single Electron’s Tiny Leap Sets Off ‘Molecular Sunscreen’ Response” 


    SLAC Lab

    June 22, 2017
    Glennda Chui

    1
    Thymine – the molecule illustrated in the foreground – is one of the four basic building blocks that make up the double helix of DNA. It’s such a strong absorber of ultraviolet light that the UV in sunlight should deactivate it, yet this does not happen. Researchers used an X-ray laser at SLAC National Accelerator Laboratory to observe the infinitesimal leap of a single electron that sets off a protective response in thymine molecules, allowing them to shake off UV damage. (Greg Stewart/SLAC National Accelerator Laboratory)

    In experiments at the Department of Energy’s SLAC National Accelerator Laboratory, scientists were able to see the first step of a process that protects a DNA building block called thymine from sun damage: When it’s hit with ultraviolet light, a single electron jumps into a slightly higher orbit around the nucleus of a single oxygen atom.

    This infinitesimal leap sets off a response that stretches one of thymine’s chemical bonds and snaps it back into place, creating vibrations that harmlessly dissipate the energy of incoming ultraviolet light so it doesn’t cause mutations.

    The technique used to observe this tiny switch-flip at SLAC’s Linac Coherent Light Source (LCLS) X-ray free-electron laser can be applied to almost any organic molecule that responds to light – whether that light is a good thing, as in photosynthesis or human vision, or a bad thing, as in skin cancer, the scientists said. They described the study in Nature Communications today.

    SLAC/LCLS

    “All of these light-sensitive organic molecules tend to absorb light in the ultraviolet. That’s not only why you get sunburn, but it’s also why your plastic eyeglass lenses offer some UV protection,” said Phil Bucksbaum, a professor at SLAC and Stanford University and director of the Stanford PULSE Institute at SLAC. “You can even see these effects in plastic lawn furniture – after a couple of seasons it can become brittle and discolored simply due to the fact that the plastic was absorbing ultraviolet light all the time, and the way it absorbs sun results in damage to its chemical bonds.”

    Catching Electrons in Action

    Thymine and the other three DNA building blocks also strongly absorb ultraviolet light, which can trigger mutations and skin cancer, yet these molecules seem to get by with minimal damage. In 2014, a team led by Markus Guehr ­– then a SLAC senior staff scientist and now on the faculty of the University of Potsdam in Germany – reported that they had found the answer: The stretch-snap of a single bond and resulting energy-dissipating vibrations, which took place within 200 femtoseconds, or millionths of a billionth of a second after UV light exposure.

    But what made the bond stretch? The team knew the answer had to involve electrons, which are responsible for forming, changing and breaking bonds between atoms. So they devised an ingenious way to catch the specific electron movements that trigger the protective response.

    It relied on the fact that electrons don’t orbit an atom’s nucleus in neat concentric circles, like planets orbiting a sun, but rather in fuzzy clouds that take a different shape depending on how far they are from the nucleus. Some of these orbitals are in fact like a fuzzy sphere; others look a little like barbells or the start of a balloon animal. You can see examples here.

    2
    No image caption or credit, but there is a comment,
    “I see the distribution in different orbitals. So if for example I take the S orbitals, they are all just a sphere. So wont the 2S orbital overlap with the 1S overlap, making the electrons in each orbital “meet” at some point? Or have I misunderstood something?”

    Strong Signal Could Solve Long-Standing Debate

    For this new experiment, the scientists hit thymine molecules with a pulse of UV laser light and tuned the energy of the LCLS X-ray laser pulses so they would home in on the response of the oxygen atom that’s at one end of the stretching, snapping bond.

    The energy from the UV light excited one of the atom’s electrons to jump into a higher orbital. This left the atom in a sort of tippy state where just a little more energy would boost a second electron into a higher orbital; and that second jump is what sets off the protective response, changing the shape of the molecule just enough to stretch the bond.

    The first jump, which was previously known to happen, is difficult to detect because the electron winds up in a rather diffuse orbital cloud, Guehr said. But the second, which had never been observed before, was much easier to spot because that electron ended up in an orbital with a distinctive shape that gave off a big signal.

    “Although this was a very tiny electron movement, the signal kind of jumped out at us in the experiment,” Guehr said. “I always had a feeling this would be a strong transition, just intuitively, but when we saw this come in it was a special moment, one of the best moments an experimentalist can have.”

    Settling a Longstanding Debate

    Study lead author Thomas Wolf, an associate staff scientist at SLAC, said the results should settle a longstanding debate about how long after UV exposure the protective response kicks in: It happens 60 femtoseconds after UV light hits. This time span is important, he said, because the longer the atom spends in the tippy state between the first jump and the second, the more likely it is to undergo some sort of reaction that could damage the molecule.

    Henrik Koch, a theorist at NTNU in Norway who was a guest professor at Stanford at the time, led the study with Guehr. He led the effort to model, understand and interpret what happened in the experiment, and he participated in it to an unusual extent, Guehr said.

    “He is extremely experienced in applying theory to methodology development, and he had this curiosity to bring this to our experiment,” Guehr said. “He was so fascinated by this research that he did something completely untypical of a theorist – he came to LCLS, into the control room, and he wanted to see the data coming in. I found that completely amazing and very motivating. It turned out that some of my previous thinking was completely right but other aspects were completely wrong, and Henrik did the right theory at the right level so we could learn from it.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 5:09 pm on June 20, 2017 Permalink | Reply
    Tags: , , In order to use the limited beam time and the precious sample material more efficiently the team developed a new method., Micro-patterned chip containing thousands of tiny pores to hold the protein crystals, SLAC LCLS, Speed up protein analysis, Structural biology, , X-ray free-electron laser,   

    From SLAC: “SLAC Experiment is First to Decipher Atomic Structure of an Intact Virus with an X-ray Laser” 


    SLAC Lab

    June 20, 2017

    1
    Surface structure of the bovine enterovirus 2. The three virus proteins are color-coded. (Jingshan Ren/University of Oxford)

    A ground-breaking experimental method developed by an international research team will substantially speed up protein analysis.

    An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team led by Alke Meents, a scientist at Germany’s DESY lab, reports in the journal Nature Methods.

    The researchers tested their method with the Linac Coherent Light Source (LCLS) X-ray free-electron laser at the Department of Energy’s SLAC National Accelerator Laboratory. Now they are working to increase the capacity and speed of the technique in anticipation of future experiments at the European XFEL X-ray free-electron laser, which is just going into operation near Hamburg, Germany.

    SLAC/LCLS

    European XFEL

    “This is a much-welcome and important technological development that will greatly optimize data collection at LCLS and other X-ray free-electron lasers for certain classes of challenging experiments,” says co-author Roberto Alonso Mori, a staff scientist in the LCLS hard X-ray group. “The same technology could be used not only for biological science but could also help data collection in other areas.”

    2
    Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. (Philip Roedig/DESY)

    A Well-Rounded View of Life

    In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of fundamental biological processes, such as the way substances are transported in and out of a cell, and can also inform drug development.

    “Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, director of life sciences at the Diamond Light Source synchrotron facility in the United Kingdom and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defense for the cell to make the virus incapable of attacking it.”

    X-ray crystallography is by far the most prolific tool used by structural biologists and has already been used to determine the structure of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

    “X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” says co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through an X-ray laser beam that pulses in a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

    This method is very successful and has already been used to determine the structure of more than 80 biomolecules, the researchers point out in their paper. However, most of the sample material is wasted. “The hit rate is typically less than 2 percent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beam time and significant amounts of sample material.

    Protein Crystals on a Chip

    In order to use the limited beam time and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

    The research team tested its method on two virus samples using SLAC’s LCLS X-ray laser, which produces 120 pulses per second. They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that causes miscarriages, stillbirths and infertility in cattle, and which is very difficult to crystallise.

    In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to 9 percent, five times the hit rate of the previous method. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from other experiments – down to a scale of 2.3 angstroms.

    “To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents says. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanoliters, or billionths of a liter, we managed using crystals that were more than 10 times smaller, having a total volume of just 0.23 nanoliters.”

    This experiment was conducted at room temperature; while rapidly cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen and in a second test, the researchers studied a viral protein called polyhedrin that makes up a viral occlusion body — a container used by certain virus species to protect up to several thousand virus particles at a time against environmental influences so they can remain intact much longer.

    From Room Temperature to a Deep Chill

    For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 percent. In just 10 minutes they recorded more than enough diffraction images to determine the protein structure to within 2.4 angstroms.

    “For the structure of polyhedrin, we only had to scan a single chip that was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

    “Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the European XFEL, which will be able to produce up to 27,000 X-ray laser pulses per second, as well as an upgraded LCLS that is scheduled to come on line in the early 2020s and produce up to a million pulses per second. Furthermore, the next generation of chips will expose only those micropores that are targeted for analysis, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

    Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being on Diamond’s I02 and I24 beamlines. Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, Lawrence Berkeley National Laboratory and SLAC were also involved in the research. LCLS is a DOE Office of Science User Facility.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.
    i1

     
  • richardmitnick 12:01 pm on June 19, 2017 Permalink | Reply
    Tags: , , , , First atomic structure of an intact virus deciphered with an X-ray laser, SLAC LCLS,   

    From DESY: “First atomic structure of an intact virus deciphered with an X-ray laser” 

    DESY
    DESY

    2017/06/19

    Groundbreaking experimental method will speed up protein analysis substantially.

    1
    Surface structure of the bovine enterovirus 2, the three virus proteins are colour coded. Credit: Jingshan Ren, University of Oxford

    An international team of scientists has for the first time used an X-ray free-electron laser to unravel the structure of an intact virus particle on the atomic level. The method used dramatically reduces the amount of virus material required, while also allowing the investigations to be carried out several times faster than before. This opens up entirely new research opportunities, as the research team lead by DESY scientist Alke Meents reports in the journal Nature Methods.

    In the field known as structural biology, scientists examine the three-dimensional structure of biological molecules in order to work out how they function. This knowledge enhances our understanding of the fundamental biological processes taking place inside organisms, such as the way in which substances are transported in and out of a cell, and can also be used to develop new drugs.

    “Knowing the three-dimensional structure of a molecule like a protein gives great insight into its biological behaviour,” explains co-author David Stuart, Director of Life Sciences at the synchrotron facility Diamond Light Source in the UK and a professor at the University of Oxford. “One example is how understanding the structure of a protein that a virus uses to ‘hook’ onto a cell could mean that we’re able to design a defence for the cell to make the virus incapable of attacking it.”

    X-ray crystallography is by far the most prolific tool used by structural biologists and has already revealed the structures of thousands of biological molecules. Tiny crystals of the protein of interest are grown, and then illuminated using high-energy X-rays. The crystals diffract the X-rays in characteristic ways so that the resulting diffraction patterns can be used to deduce the spatial structure of the crystal – and hence of its components – on the atomic scale. However, protein crystals are nowhere near as stable and sturdy as salt crystals, for example. They are difficult to grow, often remaining tiny, and are easily damaged by the X-rays.

    “X-ray lasers have opened up a new path to protein crystallography, because their extremely intense pulses can be used to analyse even extremely tiny crystals that would not produce a sufficiently bright diffraction image using other X-ray sources,” adds co-author Armin Wagner from Diamond Light Source. However, each of these microcrystals can only produce a single diffraction image before it evaporates as a result of the X-ray pulse. To perform the structural analysis, though, hundreds or even thousands of diffraction images are needed. In such experiments, scientists therefore inject a fine liquid jet of protein crystals through a pulsed X-ray laser, which releases a rapid sequence of extremely short bursts. Each time an X-ray pulse happens to strike a microcrystal, a diffraction image is produced and recorded.

    This method is very successful and has already been used to determine the structure of more than 80 biomolecules. However, most of the sample material is wasted. “The hit rate is typically less than two per cent of pulses, so most of the precious microcrystals end up unused in the collection container,” says Meents, who is based at the Center for Free-Electron Laser Science (CFEL) in Hamburg, a cooperation of DESY, the University of Hamburg and the German Max Planck Society. The standard method therefore typically requires several hours of beamtime and significant amounts of sample material.

    3
    Micrograph of the microstructured chip, loaded with crystals for the investigation. Each square is a tiny crystal. Credit: Philip Roedig, DESY

    n order to use the limited beamtime and the precious sample material more efficiently, the team developed a new method. The scientists use a micro-patterned chip containing thousands of tiny pores to hold the protein crystals. The X-ray laser then scans the chip line by line, and ideally this allows a diffraction image to be recorded for each pulse of the laser.

    The research team tested its method on two different virus samples using the LCLS X-ray laser at the SLAC National Accelerator Laboratory in the US, which produces 120 pulses per second.

    SLAC/LCLS

    They loaded their sample holder with a small amount of microcrystals of the bovine enterovirus 2 (BEV2), a virus that can cause miscarriages, stillbirths, and infertility in cattle, and which is very difficult to crystallise.

    In this experiment, the scientists achieved a hit rate – where the X-ray laser successfully targeted the crystal – of up to nine per cent. Within just 14 minutes they had collected enough data to determine the correct structure of the virus – which was already known from experiments at other X-ray light sources – down to a scale of 0.23 nanometres (millionths of a millimetre).

    “To the best of our knowledge, this is the first time the atomic structure of an intact virus particle has been determined using an X-ray laser,” Meents points out. “Whereas earlier methods at other X-ray light sources required crystals with a total volume of 3.5 nanolitres, we managed using crystals that were more than ten times smaller, having a total volume of just 0.23 nanolitres.”

    This experiment was conducted at room temperature. While cooling the protein crystals would protect them to some extent from radiation damage, this is not generally feasible when working with extremely sensitive virus crystals. Crystals of isolated virus proteins can, however, be frozen, and in a second test, the researchers studied the viral protein polyhedrin that makes up a viral occlusion body for up to several thousands of virus particles of certain species. The virus particles use these containers to protect themselves against environmental influences and are therefore able to remain intact for much longer times.

    4
    Schematic of the experimental set-up: The chip loaded with nanocrystals is scanned by the fine X-ray beam (green) pore by pore. Ideally, each crystal produces a distinctive diffraction pattern. Credit: Philip Roedig, DESY

    For the second test, the scientist loaded their chip with polyhedrin crystals and examined them using the X-ray laser while keeping the chip at temperatures below minus 180 degrees Celsius. Here, the scientists achieved a hit rate of up to 90 per cent. In just ten minutes they had recorded more than enough diffraction images to determine the protein structure to within 0.24 nanometres. “For the structure of polyhedrin, we only had to scan a single chip which was loaded with four micrograms of protein crystals; that is orders of magnitude less than the amount that would normally be needed,” explains Meents.

    “Our approach not only reduces the data collection time and the quantity of the sample needed, it also opens up the opportunity of analysing entire viruses using X-ray lasers,” Meents sums up. The scientists now want to increase the capacity of their chip by a factor of ten, from 22,500 to some 200,000 micropores, and further increase the scanning speed to up to one thousand samples per second. This would better exploit the potential of the new X-ray free-electron laser European XFEL, which is just going into operation in the Hamburg region and which will be able to produce up to 27,000 pulses per second.

    European XFEL

    Furthermore, the next generation of chips will only expose those micropores that are currently being analysed, to prevent the remaining crystals from being damaged by scattered radiation from the X-ray laser.

    Researchers from the University of Oxford, the University of Eastern Finland, the Swiss Paul Scherrer Institute, the Lawrence Berkeley National Laboratory in the US and SLAC were also involved in the research. Diamond scientists have collaborated with the team at DESY, with much of the development and testing of the micro-patterned chip being done on Diamond’s I02 and I24 beamlines.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    desi

    DESY is one of the world’s leading accelerator centres. Researchers use the large-scale facilities at DESY to explore the microcosm in all its variety – from the interactions of tiny elementary particles and the behaviour of new types of nanomaterials to biomolecular processes that are essential to life. The accelerators and detectors that DESY develops and builds are unique research tools. The facilities generate the world’s most intense X-ray light, accelerate particles to record energies and open completely new windows onto the universe. 
That makes DESY not only a magnet for more than 3000 guest researchers from over 40 countries every year, but also a coveted partner for national and international cooperations. Committed young researchers find an exciting interdisciplinary setting at DESY. The research centre offers specialized training for a large number of professions. DESY cooperates with industry and business to promote new technologies that will benefit society and encourage innovations. This also benefits the metropolitan regions of the two DESY locations, Hamburg and Zeuthen near Berlin.

     
c
Compose new post
j
Next post/Next comment
k
Previous post/Previous comment
r
Reply
e
Edit
o
Show/Hide comments
t
Go to top
l
Go to login
h
Show/Hide help
shift + esc
Cancel
%d bloggers like this: