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Chemists ID Catalytic 'Key' for Converting CO2 to Methanol

Results from experiments and computational modeling studies that definitively identify the "active site" of a catalyst commonly used for making methanol from CO2 will guide the design of improved catalysts for transforming this pollutant to useful chemicals.

Cryo-Electron Microscopy Achieves Unprecedented Resolution Using New Computational Methods

Cryo-electron microscopy (cryo-EM)--which enables the visualization of viruses, proteins, and other biological structures at the molecular level--is a critical tool used to advance biochemical knowledge. Now Berkeley Lab researchers have extended cryo-EM's impact further by developing a new computational algorithm instrumental in constructing a 3-D atomic-scale model of bacteriophage P22 for the first time.

New Study Maps Space Dust in 3-D

A new Berkeley Lab-led study provides detailed 3-D views of space dust in the Milky Way, which could help us understand the properties of this dust and how it affects views of distant objects.

Single-Angle Ptychography Allows 3D Imaging of Stressed Materials

Scientists have used a new X-ray diffraction technique called Bragg single-angle ptychography to get a clear picture of how planes of atoms shift and squeeze under stress.

New Feedback System Could Allow Greater Control Over Fusion Plasma

A physicist has created a new system that will let scientists control the energy and rotation of plasma in real time in a doughnut-shaped machine known as a tokamak.

Towards Super-Efficient, Ultra-Thin Silicon Solar Cells

Researchers from Ames Laboratory used supercomputers at NERSC to evaluate a novel approach for creating more energy-efficient ultra-thin crystalline silicon solar cells by optimizing nanophotonic light trapping.

Study IDs Link Between Sugar Signaling and Regulation of Oil Production in Plants

UPTON, NY--Even plants have to live on an energy budget. While they're known for converting solar energy into chemical energy in the form of sugars, plants have sophisticated biochemical mechanisms for regulating how they spend that energy. Making oils costs a lot. By exploring the details of this delicate energy balance, a group of scientists from the U.

High-Energy Electrons Probe Ultrafast Atomic Motion

A new technique synchronized high-energy electrons with an ultrafast laser pulse to probe how vibrational states of atoms change in time.

Rare Earth Recycling

A new energy-efficient separation of rare earth elements could provide a new domestic source of critical materials.

Two-Dimensional MXene Materials Get Their Close-Up

Researchers have long sought electrically conductive materials for economical energy-storage devices. Two-dimensional (2D) ceramics called MXenes are contenders.


Three SLAC Employees Awarded Lab's Highest Honor

At a March 7 ceremony, three employees of the Department of Energy's SLAC National Accelerator Laboratory were awarded the lab's highest honor ­- the SLAC Director's Award.

Dan Sinars Represents Sandia in First Energy Leadership Class

Dan Sinars, a senior manager in Sandia National Laboratories' pulsed power center, which built and operates the Z facility, is the sole representative from a nuclear weapons lab in a new Department of Energy leadership program that recently visited Sandia.

ORNL, HTS International Corporation to Collaborate on Manufacturing Research

HTS International Corporation and the Department of Energy's Oak Ridge National Laboratory have signed an agreement to explore potential collaborations in advanced manufacturing research.

Jefferson Lab Director Honored with Energy Secretary Award

Hugh Montgomery, director of the Department of Energy's Thomas Jefferson National Accelerator Facility (Jefferson Lab), was awarded The Secretary's Distinguished Service Award by the Secretary of Energy earlier this year.

New Projects to Make Geothermal Energy More Economically Attractive

Geothermal energy, a clean, renewable source of energy produced by the heat of the earth, provides about 6 percent of California's total power. That number could be much higher if associated costs were lower. Now scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have launched two California Energy Commission-funded projects aimed at making geothermal energy more cost-effective to deploy and operate.

Southern Research Project Advances Novel CO2 Utilization Strategy

The U.S. Department of Energy's Office of Fossil Energy has awarded Southern Research nearly $800,000 for a project that targets a more cost-efficient and environmentally friendly method of producing some of the most important chemicals used in manufacturing.

Harker School Wins 2017 SLAC Regional Science Bowl Competition

After losing its first match of the day to the defending champions, The Harker School's team won 10 consecutive rounds to claim victory in the annual SLAC Regional DOE Science Bowl on Saturday, Feb. 11.

Francis Alexander Named Deputy Director of Brookhaven Lab's Computational Science Initiative

Alexander brings extensive management and leadership experience in computational science research to the position.

Kalinin, Paranthaman Elected Materials Research Society Fellows

Two researchers at Oak Ridge National Laboratory, Sergei Kalinin and Mariappan Parans Paranthaman, have been elected fellows of the Materials Research Society.

Two PNNL Researchers Elected to Membership in the National Academy of Engineering

Two scientists at the Pacific Northwest National Laboratory will become members of the prestigious National Academy of Engineering.


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Rare Earth Recycling

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Modeling the "Flicker" of Gluons in Subatomic Smashups

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Rare Nickel Atom Has "Doubly Magic" Structure

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Microbial Activity in the Subsurface Contributes to Greenhouse Gas Fluxes

Natural carbon dioxide production from deep subsurface soils contributes significantly to emissions, even in a semiarid floodplain.

Stretching a Metal Into an Insulator

Straining a thin film controllably allows tuning of the materials' magnetic, electronic, and catalytic properties, essential for new energy and electronic devices.

How Moisture Affects the Way Soil Microbes Breathe

Study models soil-pore features that hold or release carbon dioxide.

ARM Data Is for the Birds

Scientists use LIDAR and radar data to study bird migration patterns, thanks to the Atmospheric Radiation Measurement (ARM) Climate Research Facility.

The Future of Coastal Flooding

Better storm surge prediction capabilities could help reduce the impacts of extreme weather events, such as hurricanes.

Estimating Global Energy Use for Water-Related Processes

Scientists find that water-related energy consumption is increasing across the globe, with pronounced differences across regions and sectors.


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Hugging Hemes Help Electrons Hop

Article ID: 612456

Released: 2014-01-15 15:15:00

Source Newsroom: Pacific Northwest National Laboratory

  • Credit: Cortland Johnson (PNNL) and Julian Breuer

    Numbered heme groups (in color) lie within MtrF protein's framework (in gray) and shuttle electrons from one end of the protein to the other.

Mary Beckman, mary.beckman@pnnl.gov, (509) 375-3688

RICHLAND, Wash. -- Researchers simulating how certain bacteria run electrical current through tiny molecular wires have discovered a secret Nature uses for electron travel. The results are key to understanding how the bacteria do chemistry in the ground, and will help researchers use them in microbial fuel cells, batteries, or for turning waste into electricity.

Within the bacteria's protein-based wire, molecular groups called hemes communicate with each other to allow electrons to hop along the chain like stepping stones. The researchers found that evolution has set the protein up so that, generally, when the electron's drive to hop is high, the heme stepping stones are less tightly connected, like being farther apart; when the drive to hop is low, the hemes are more closely connected, like being closer together. The outcome is an even electron flow along the wire.

This is the first time scientists have seen this evolutionary design principle for electron transport, the researchers reported Jan. 2 in Proceedings of the National Academy of Sciences Early Edition Online.

"We were perplexed at how weak the thermodynamic driving force was between some of these hemes," said geochemist Kevin Rosso of the Department of Energy's Pacific Northwest National Laboratory. "But it turns out those pairs of hemes are essentially hugging each other. When the driving force is strong between hemes, they are only shaking hands. We've never seen this compensation scheme before, but it seems that the purpose is to allow the protein to transfer electrons with a steady flow along heme wires."

Living Wires

Certain bacteria breathe using metal like people use oxygen. In the process, these bacteria steal electrons from carbon and ultimately transfer the electrons to metals or minerals in the ground. They do this by conducting electricity along molecular wires built into proteins, moving internal electrons to the outside of their cells. Researchers hope to use these bacteria in little biologic batteries or fuel cells.

But a living wire is not the same as those that make up our powerlines. Electrons in powerlines hurtle down the wire, moving smoothly from metal atom to metal atom. Electrons traveling in a living wire must get from one complex heme group to the next. The hemes are situated within a protein, and not all hemes are made the same.

Some hemes hold onto electrons tightly and others let electrons slip away easily. Depending on how the hemes are lined up, this can create energetic hills that electrons have a hard time climbing over, or energetic valleys that electrons easily march across.

Some hemes, such as those that carry oxygen in people's red blood cells, are well-studied. The hemes and proteins creating a current in bacteria, though, have only been coming to light within the last few years. Recently, researchers figured out what a particular protein -- MtrF -- that makes up a molecular wire looks like, but that information alone is not enough to determine how the electrons traverse the chain of internal heme groups.

So, armed with the structure of the protein, Rosso and colleagues Jochen Blumberger and Marian Breuer from the University College London used high-powered computers to simulate the positions and movement of the hemes in MtrF and how they transfer electrons between themselves.

Electron Crossroads

Using resources at both the UK's High Performance Computing Facility and EMSL, the Environmental Molecular Sciences Laboratory at PNNL, the team first modeled the average position of the 10 hemes within MtrF. Eight of the hemes run down the center of the protein. The remaining two hemes branch off the main eight, creating a four-heme road that crosses the middle of the protein.

Because hemes have to pass electrons to each other, the team examined them in pairs. The team found that MtrF arranges its heme pairs in one of three ways: perpendicular to each other, side-by-side, or stacked on top of each other. Each arrangement positions the hemes at different distances from and orientations to each other.

Then the team gauged how urgently an electron wants to get from one heme to the next by determining the theoretical "Gibbs free energy" between the pairs. This value is an indicator of the driving force of the electrons.

The team found that instead of a smooth ride through the protein, electrons lurch through hemes: Sometimes the driving force makes the electrons march across a valley and the electrons move quickly. In other pairs the electrons face a hill, and electron travel gets delayed.

Mapping how tightly hemes couple to each other along with the driving force values, the team found that hemes were less tightly coupled when electrons enjoyed traipsing across a valley and more tightly coupled when electrons had to slog uphill.

"The computer simulations allowed us to break the wire down into how each step is possible and how fast each step is. Then we saw that the protein arranges its hemes in weak and strong couplings to compensate for the energetic hills and valleys," said Rosso. "This is one way to make the electron hops consistent to efficiently get them where they need to go."

This compensation scheme led the team to wonder why the hills and valleys are there in the first place.

"We think the variation in driving force between the hills and the valleys helps the protein interact with other components in the environment,” said Rosso. The tops of the hills could be exit points to higher energy electron acceptors in the environment, such as molecules that shuttle electrons elsewhere.

Scientists don't yet know how multiple heme proteins -- including others beyond MtrF – work in concert to make these molecular wires connect end-to-end, but the results give hints as to which hemes are possible entry and exit points in MtrF. So the results also give clues to how multiple proteins might be connected.

This work was supported by the Department of Energy Office of Science. Support for use of the UK’s High Performance Computing Facility was provided by the UK’s Engineering and Physical Sciences Research Council. Additional support was provided by the Royal Society.

###

Reference: Marian Breuer, Kevin M. Rosso, and Jochen Blumberger. Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials, Proc Natl Acad Sci U S A, Early Edition online January 2, 2014. doi:10.1073/pnas.1316156111. (http://www.pnas.org/content/early/2013/12/26/1316156111.abstract)

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