DOE News
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    The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
    • 2020-05-20 12:55:32
    • Article ID: 731889

    Supercomputing Aids Scientists Seeking Therapies for Deadly Bacterial Disease

    Summit captures "in between" stages of bacterial protein movements, giving researchers hope for finding drug targets for rabbit fever

    • Credit: Abhishek Singharoy, Arizona State University

      Flpp3 structures from NMR (red) and XRC (blue), from 2MU4 and 6PNY in the Protein Data Bank, respectively. There is no cavity observed in the XRC structure, which would appear as a red, semi-transparent surface, but a cavity is shown in the NMR structure (blue, semi-transparent surface).

    Francisella tularensis, a bacterium that causes the illness tularemia (also known as “rabbit fever”), is one of the most hostile organisms on the planet. Once the bacterium enters the body and tularemia sets in, an infected person can experience a range of symptoms, from ulcers to tonsillitis to pneumonia that can turn fatal.

    The bacterium is spread through contact with infected animals, drinking contaminated water, tick and deer fly bites, and inhalation in certain agricultural environments. It also the potential to be a serious bioterrorism threat; it can be easily spread via aerosol, and as few as 10 organisms can cause the disease. Despite its virulence, scientists have not identified the best target in Francisella’s genetic material for a vaccine. Understanding the protein structures that are encoded by the bacterium’s genetic material is crucial for developing vaccines and treatments against these structures, but getting a detailed look at them has been challenging because the bacterium is difficult to isolate.

    Now, a team of scientists led by Abhishek Singharoy, assistant professor at Arizona State University (ASU), has used the IBM AC922 Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF) to simulate the structure of a possible drug target, a lipoprotein (or fat-transporting protein) called Francisella lipoprotein 3 (Flpp3), to reveal the different possible states the protein can exist in. The simulations were guided by experiments that employed different methods to understand the protein’s structure.

    “When a drug discovery pipeline is created, you need information for the druggability of multiple conformations, or states,” Singharoy said. “You might only find a handful of conformations that are druggable.”

    The team has since begun virtually screening compounds that might easily interfere with the Flpp3 protein and prevent Francisella from spreading. Identifying drugs that could bind to Flpp3 is the next step towards preparation for biological attacks.

    Summit settles a mystery

    Among the methods scientists can use to determine the structural states of molecules are nuclear magnetic resonance (NMR) and x-ray crystallography (XRC). NMR uses a varying magnetic field to calculate the distance between atoms and identify compounds, and XRC uses x-ray diffraction images from crystals, formed by packing together molecules, to determine the molecular structure.

    Scientists previously identified Flpp3 as a protein that can determine the virulence of tularemia, and in 2015 Petra Fromme, director of the Biodesign Center for Applied Structural Discovery at ASU, and ASU graduate student James Zook used NMR to capture its structure. Then, to get an even better look at Flpp3’s structure, they took the protein to the Linac Coherent Light Source (LCLS), a US Department of Energy (DOE) Office of Science User Facility at the SLAC National Accelerator Laboratory. The team performed XRC on the protein using the LCLS, and results showed a difference in the NMR and XRC structures—one showed the open protein and the other showed the closed protein. But what was happening in the middle?

    “In the body, proteins spontaneously open and close, but in an experiment, you only get one or the other,” said Josh Vermaas, a computational scientist in the Scientific Computing Group at the OLCF. “Identifying states along the process between those two end states allows scientists to target the in between states as well or prevent it from opening or closing.” 

    After earning computing time under the Innovative Novel and Computational Impact on Theory and Experiment program, the team gained access to Summit, a 200-petaflop system at the OLCF, a DOE Office of Science User Facility located at DOE’s Oak Ridge National Laboratory. Using a computational method called molecular dynamics—which calculates the movement of molecules in time and space—Singharoy, with ASU postdoctoral researchers Mrinal Shekhar and Chitrak Gupta, modeled the mystery states between the XRC and NMR results. After performing thousands of simulations consisting of more than 100,000 atoms each, the team found that the protein has a cavity that a drug molecule could take advantage of and fill while the protein is busy opening or closing.

    “Sometimes, drugs have to have the right shape to fit the pocket that’s formed by the protein,” Vermaas said. “A lot of drugs that bind to membrane proteins will activate a protein or turn it off or impact it one way or another.”

    Discovery in silico

    Armed with an exhaustive set of models for Flpp3, the team screened drug compounds using the ZINC database, a collection of commercially available compounds. After finding one possible molecule and then modifying it to increase possible bonding sites, the team devised a drug compound that specifically inserts itself deep into the protein cavity of Flpp3.

    “We found that the different states of this protein can be overcome at room temperature, meaning this is something that can easily be studied in a laboratory setting,” Singharoy said.

    “The next step is to investigate this as not only a binding partner to the protein but also as an agent against tularemia.”

    The team hopes that the new understanding of the protein’s different conformations, combined with the virtual screening, will lead to antibiotics that can target tularemia. Future studies will look at the antimicrobial effects of the drug compounds that bind to Flppp3.

    “Ultimately, these results are ultimately allowing us to look at drug targets in a more realistic way than ever before,” Singharoy said.

    Related Publication: Zook, J. et al. “XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia.” Structure 28 (2020): 1–8. doi:10.1016/j.str.2020.02.005.

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    Scientists Successfully Demonstrate a New Experiment in the Search for Theorized 'Neutrinoless' Process

    Scientists Successfully Demonstrate a New Experiment in the Search for Theorized 'Neutrinoless' Process

    Nuclear physicists affiliated with Berkeley Lab played a leading role in analyzing data for a demonstration experiment in France that has achieved record precision for a specialized detector material.

    Argonne soil carbon research reduces uncertainty in predicting climate change impacts

    Argonne soil carbon research reduces uncertainty in predicting climate change impacts

    DOE and USDA researchers use new global models to study how environmental controllers affect soil organic carbon, changes in which can alter atmospheric carbon concentrations and affect climate. Predictions could benefit industry mitigation plans.

    Learning more about particle collisions with machine learning

    Learning more about particle collisions with machine learning

    A team of Argonne scientists has devised a machine learning algorithm that calculates, with low computational time, how the ATLAS detector in the Large Hadron Collider would respond to the ten times more data expected with a planned upgrade in 2027.

    New cathode coating extends lithium-ion battery life, boosts safety

    New cathode coating extends lithium-ion battery life, boosts safety

    The U.S. Department of Energy's Argonne National Laboratory, in collaboration with Hong Kong University of Science and Technology, has developed a new particle-level cathode coating for lithium ion batteries meant to increase their life and safety.

    Scientists Dive Deep Into Hidden World of Quantum States

    Scientists Dive Deep Into Hidden World of Quantum States

    A research team led by the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a technique that could lead to new electronic materials that surpass the limitations imposed by Moore's Law.

    Precise Measurement of Pions Confirms Understanding 
of Fundamental Symmetry

    Precise Measurement of Pions Confirms Understanding of Fundamental Symmetry

    Nuclear physicists have announced the most precise measurement yet of the ultra-short lifetime of the neutral pion. The result is an important validation of our understanding of the theory of quantum chromodynamics, which describes the makeup of ordinary matter. The research, carried out at the Department of Energy's Thomas Jefferson National Accelerator Facility, was recently published in the journal Science.

    Story Tips: Predicting fire risk, solid state stability check and images in a flash

    Story Tips: Predicting fire risk, solid state stability check and images in a flash

    ORNL Story Tips: Predicting fire risk, solid state stability check and images in a flash

    Summit Helps Predict Molecular Breakups

    Summit Helps Predict Molecular Breakups

    A team used the Summit supercomputer to simulate transition metal systems--such as copper bound to molecules of nitrogen, dihydrogen, or water--and correctly predicted the amount of energy required to break apart dozens of molecular systems, paving the way for a greater understanding of these materials.

    Carbon-loving materials designed to reduce industrial emissions

    Carbon-loving materials designed to reduce industrial emissions

    Researchers at the Department of Energy's Oak Ridge National Laboratory and the University of Tennessee, Knoxville, are advancing gas membrane materials to expand practical technology options for reducing industrial carbon emissions.

    Science Snapshots July 2020

    Science Snapshots July 2020

    Berkeley Lab Science Snapshots July 2020


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    Fundamental Exploration Into Future Clean Energy Technologies Receives DOE Support

    Fundamental Exploration Into Future Clean Energy Technologies Receives DOE Support

    The U.S. Department of Energy recently awarded $65 million in grants to support research that will advance safe, reliable, and clean nuclear energy. Among those projects are two led by Rensselaer Polytechnic Institute, which received a combined total of $1.2 million.

    Argonne to explore how digital twins may transform nuclear energy with $8 million from ARPA-E's GEMINA program

    Argonne to explore how digital twins may transform nuclear energy with $8 million from ARPA-E's GEMINA program

    ARPA-E's GEMINA funding will allow Argonne's nuclear scientists to partner with industry and develop tools for the advanced reactors of tomorrow.

    Brookhaven and Forge Nano to Mature Noble Gas-Trapping Technology

    Brookhaven and Forge Nano to Mature Noble Gas-Trapping Technology

    Through DOE's Technology Commercialization Fund, the national lab-startup team will develop "nanocages" for nuclear applications.

    Chicago Quantum Exchange welcomes seven new partners in tech, computing and finance, to advance research and training

    Chicago Quantum Exchange welcomes seven new partners in tech, computing and finance, to advance research and training

    The Chicago-based research hub expands to include 13 total industry leaders in tech, computing, finance.

    EIC Center at Jefferson Lab Announces Six New Research Awards

    EIC Center at Jefferson Lab Announces Six New Research Awards

    The Electron-Ion Collider Center at the Department of Energy's Thomas Jefferson National Accelerator Facility (EIC Center at Jefferson Lab) has announced the winners of six international fellowships. The fellows will pursue research over the next year related to advancing the science program of the Electron-Ion Collider (EIC), a one-of-a-kind nuclear physics research facility to be built over the next decade at DOE's Brookhaven National Laboratory in Upton, New York, in partnership with Jefferson Lab.

    Department of Energy awards $3.15 million to Argonne to support collaborations with industry

    Department of Energy awards $3.15 million to Argonne to support collaborations with industry

    The U.S. Department of Energy (DOE) announced more than $33 million in funding for 82 projects aimed at advancing commercialization of promising energy technologies and strengthening partnerships between DOE's National Laboratories and private-sector companies.

    Analyzing Matter's Building Blocks

    Analyzing Matter's Building Blocks

    Nobuo Sato is working to put the know in femto. He's just been awarded a five-year, multimillion dollar research grant by the Department of Energy to develop a "FemtoAnalyzer" that will help nuclear physicists image the three-dimensional internal structure of protons and neutrons. Now, Sato is among 76 scientists nationwide who have been awarded a grant through the DOE Office of Science's Early Career Research Program to pursue their research.

    Particle Physicist Takes the Lead on Groundbreaking Electron Measurement

    Particle Physicist Takes the Lead on Groundbreaking Electron Measurement

    James "Jim" Fast has joined Jefferson Lab as the MOLLER Project Manager. MOLLER is the "Measurement of a Lepton-Lepton Electroweak Reaction" experiment that will measure the weak charge of the electron.

    Six Argonne researchers receive DOE Early Career Research Program awards

    Six Argonne researchers receive DOE Early Career Research Program awards

    Argonne scientists Michael Bishof, Maria Chan, Marco Govini, Alessandro Lovato, Bogdan Nicolae and Stefan Wild have received funding for their research as part of DOE's Early Career Research Program.

    Three Fermilab scientists receive DOE Early Career Research Awards

    Three Fermilab scientists receive DOE Early Career Research Awards

    The Department of Energy's Office of Science has selected three Fermilab scientists to receive the 2020 DOE Early Career Research Award, now in its 11th year. The prestigious award is designed to bolster the nation's scientific workforce by providing support to exceptional researchers during the crucial early years, when many scientists do their most formative work.


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    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Harvesting Energy from Light using Bio-inspired Artificial Cells

    Scientists designed and connected two different artificial cells to each other to produce molecules called ATP (adenosine triphosphate).

    Engineering Living Scaffolds for Building Materials

    Engineering Living Scaffolds for Building Materials

    Bone and mollusk shells are composite systems that combine living cells and inorganic components. This allows them to regenerate and change structure while also being very strong and durable. Borrowing from this amazing complexity, researchers have been exploring a new class of materials called engineered living materials (ELMs).

    Excavating Quantum Information Buried in Noise

    Excavating Quantum Information Buried in Noise

    Researchers developed two new methods to assess and remove error in how scientists measure quantum systems. By reducing quantum "noise" - uncertainty inherent to quantum processes - these new methods improve accuracy and precision.

    How Electrons Move in a Catastrophe

    How Electrons Move in a Catastrophe

    Lanthanum strontium manganite (LSMO) is a widely applicable material, from magnetic tunnel junctions to solid oxide fuel cells. However, when it gets thin, its behavior changes for the worse. The reason why was not known. Now, using two theoretical methods, a team determined what happens.

    When Ions and Molecules Cluster

    When Ions and Molecules Cluster

    How an ion behaves when isolated within an analytical instrument can differ from how it behaves in the environment. Now, Xue-Bin Wang at Pacific Northwest National Laboratory devised a way to bring ions and molecules together in clusters to better discover their properties and predict their behavior.

    Tune in to Tetrahedral Superstructures

    Tune in to Tetrahedral Superstructures

    Shape affects how the particles fit together and, in turn, the resulting material. For the first time, a team observed the self-assembly of nanoparticles with tetrahedral shapes.

    Tracing Interstellar Dust Back to the Solar System's Formation

    Tracing Interstellar Dust Back to the Solar System's Formation

    This study is the first to confirm dust particles pre-dating the formation of our solar system. Further study of these materials will enable a deeper understanding of the processes that formed and have since altered them.

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Investigating Materials that Can Go the Distance in Fusion Reactors

    Future fusion reactors will require materials that can withstand extreme operating conditions, including being bombarded by high-energy neutrons at high temperatures. Scientists recently irradiated titanium diboride (TiB2) in the High Flux Isotope Reactor (HFIR) to better understand the effects of fusion neutrons on performance.

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    Better 3-D Imaging of Tumors in the Breast with Less Radiation

    In breast cancer screening, an imaging technique based on nuclear medicine is currently being used as a successful secondary screening tool alongside mammography to improve the accuracy of the diagnosis. Now, a team is hoping to improve this imaging technique.

    Microbes are Metabolic Specialists

    Microbes are Metabolic Specialists

    Scientists can use genetic information to measure if microbes in the environment can perform specific ecological roles. Researchers recently analyzed the genomes of over 6,000 microbial species.


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