High-performance simulation, neutrons uncover three classes of protein motion

ScienceDaily (Oct. 2, 2011) — Molecular motion in proteins comes in three distinct classes, according to a collaboration by researchers at the Department of Energy's Oak Ridge National Laboratory and the University of Tennessee, in research reported in Physical Review Letters.

The research team, directed by ORNL-UT Governor's Chairs Jeremy Smith and Alexei Sokolov, combined high-performance computer simulation with neutron scattering experiments to understand atomic-level motions that underpin the operations of proteins.

"The analysis and interpretation of neutron scattering spectra are always difficult for complex molecules such as proteins," said Smith, who directs ORNL's Center for Molecular Biophysics. "We've performed experiments and then shown that simulation can provide a clear view of them. It allows us to see through the complexity and find out what motions are going on."

Defining the motions present -- localized diffusion, methyl group rotations and jumps -- is important as it allows scientists to think about how the motions determine the functions of proteins that are critical to all life.

"First, we found that experiment and simulation agreed perfectly with each other, which is remarkable," Smith said. "Second, the simulations told us that this type of neutron scattering can be interpreted in a very simple way."

Although the team performed its research on a particular protein called lysozyme, a natural antibacterial enzyme found in tears, saliva and egg whites, the researchers anticipate the technique will have a much broader impact in the neutron scattering community, aiding research in areas such as biofuel design or environmental remediation.

The combined simulation and neutron scattering approach should also be of use in the characterization of non-biological materials such as polymers. Smith notes that approximately half the neutron scattering experiments at ORNL's Spallation Neutron Source involve the study of motions in materials.

"These methods are of general applicability," Smith said. "Many experimentalists can now come to the ORNL's Spallation Neutron Source, measure a spectrum of whatever sample they have, and then apply this analysis in terms of three classes of motion to interpret their results."

The research was primarily conducted by ORNL's Liang Hong, with the support of Benjamin Lindner and Nikolai Smolin from ORNL. They performed neutron scattering experiments at ORNL's Spallation Neutron Source on the BASIS instrument and at the National Institute of Standards and Technology Center for Neutron Research.

The simulation component of the work was supported by ORNL's Laboratory Directed Research and Development program, while the neutron scattering component was supported by an Experimental Program to Stimulate Competitive Research (EPSCOR) grant to the University of Tennessee from the DOE Office of Science.

ORNL is managed by UT-Battelle for the Department of Energy's Office of Science.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by DOE/Oak Ridge National Laboratory.

Journal Reference:

Liang Hong, Nikolai Smolin, Benjamin Lindner, Alexei P. Sokolov, Jeremy C. Smith. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Physical Review Letters, 2011; (accepted)

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

High-performance simulation, neutrons uncover three classes of protein motion

ScienceDaily (Oct. 2, 2011) — Molecular motion in proteins comes in three distinct classes, according to a collaboration by researchers at the Department of Energy's Oak Ridge National Laboratory and the University of Tennessee, in research reported in Physical Review Letters.

The research team, directed by ORNL-UT Governor's Chairs Jeremy Smith and Alexei Sokolov, combined high-performance computer simulation with neutron scattering experiments to understand atomic-level motions that underpin the operations of proteins.

"The analysis and interpretation of neutron scattering spectra are always difficult for complex molecules such as proteins," said Smith, who directs ORNL's Center for Molecular Biophysics. "We've performed experiments and then shown that simulation can provide a clear view of them. It allows us to see through the complexity and find out what motions are going on."

Defining the motions present -- localized diffusion, methyl group rotations and jumps -- is important as it allows scientists to think about how the motions determine the functions of proteins that are critical to all life.

"First, we found that experiment and simulation agreed perfectly with each other, which is remarkable," Smith said. "Second, the simulations told us that this type of neutron scattering can be interpreted in a very simple way."

Although the team performed its research on a particular protein called lysozyme, a natural antibacterial enzyme found in tears, saliva and egg whites, the researchers anticipate the technique will have a much broader impact in the neutron scattering community, aiding research in areas such as biofuel design or environmental remediation.

The combined simulation and neutron scattering approach should also be of use in the characterization of non-biological materials such as polymers. Smith notes that approximately half the neutron scattering experiments at ORNL's Spallation Neutron Source involve the study of motions in materials.

"These methods are of general applicability," Smith said. "Many experimentalists can now come to the ORNL's Spallation Neutron Source, measure a spectrum of whatever sample they have, and then apply this analysis in terms of three classes of motion to interpret their results."

The research was primarily conducted by ORNL's Liang Hong, with the support of Benjamin Lindner and Nikolai Smolin from ORNL. They performed neutron scattering experiments at ORNL's Spallation Neutron Source on the BASIS instrument and at the National Institute of Standards and Technology Center for Neutron Research.

The simulation component of the work was supported by ORNL's Laboratory Directed Research and Development program, while the neutron scattering component was supported by an Experimental Program to Stimulate Competitive Research (EPSCOR) grant to the University of Tennessee from the DOE Office of Science.

ORNL is managed by UT-Battelle for the Department of Energy's Office of Science.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by DOE/Oak Ridge National Laboratory.

Journal Reference:

Liang Hong, Nikolai Smolin, Benjamin Lindner, Alexei P. Sokolov, Jeremy C. Smith. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Physical Review Letters, 2011; (accepted)

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Neutrons, simulations reveal details of molecule that complicates next-generation biofuels

ScienceDaily (June 16, 2011) — A first-of-its-kind combination of experiment and simulation at the Department of Energy's Oak Ridge National Laboratory is providing a close-up look at the molecule that complicates next-generation biofuels.

Lignin, a major component of plant cell walls, aggregates to form clumps, which cause problems during the production of cellulosic ethanol. The exact shape and structure of the aggregates, however, have remained largely unknown.

A team led by ORNL's Jeremy Smith revealed the surface structure of lignin aggregates down to 1 angstrom -- the equivalent of a 10 billionth of a meter or smaller than the width of a carbon atom. The team's findings were published in Physical Review E.

"We've combined neutron scattering experiments with large-scale simulations on ORNL's main supercomputer to reveal that pretreated softwood lignin aggregates are characterized by a highly folded surface," said Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee.

Lignin clumps can inhibit the conversion of biofuel feedstocks -- for example, switchgrass -- into ethanol, a renewable substitute for gasoline. When enzymes are used to release plant sugars necessary for ethanol production, the lignin aggregates bind to the enzymes and reduce the efficiency of the conversion.

Lignin's highly folded surface creates more opportunities to capture the passing enzymes than a smooth surface would. An improved understanding of the lignin aggregates will aid scientists in efforts to design a more effective pretreatment process, which in turn could lower the cost of biofuels.

"Nature has evolved a very sophisticated mechanism to protect plants against enzymatic attack," said ORNL team member Loukas Petridis. "We're trying to understand the physical basis of biomass recalcitrance -- resistance of the plants to enzymatic degradation."

The complementary techniques of simulation on ORNL's Jaguar supercomputer and neutron scattering at the lab's High Flux Isotope Reactor enabled Smith's team to resolve lignin's structure at scales ranging from 1 to 1,000 angstroms. Smith's project is the first to combine the two methods in biofuel research. "This work illustrates how state-of-the-art neutron scattering and high-performance supercomputing can be integrated to reveal structures of importance to the energy biosciences," Smith said.

The research was supported by DOE's Office of Science and used the resources of the Leadership Computing Facility at ORNL under a DOE INCITE award. Team members include ORNL's Sai Venkatesh Pingali, Volker Urban, William Heller, Hugh O'Neill and Marcus Foston and Arthur Ragauskas from Georgia Institute of Technology.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by DOE/Oak Ridge National Laboratory.

Journal Reference:

Loukas Petridis, Sai Pingali, Volker Urban, William Heller, Hugh O’Neil, Marcus Foston, Arthur Ragauskas, Jeremy Smith. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Physical Review E, 2011; 83 (6) DOI: 10.1103/PhysRevE.83.061911

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Neutrons, simulations reveal details of molecule that complicates next-generation biofuels

ScienceDaily (June 16, 2011) — A first-of-its-kind combination of experiment and simulation at the Department of Energy's Oak Ridge National Laboratory is providing a close-up look at the molecule that complicates next-generation biofuels.

Lignin, a major component of plant cell walls, aggregates to form clumps, which cause problems during the production of cellulosic ethanol. The exact shape and structure of the aggregates, however, have remained largely unknown.

A team led by ORNL's Jeremy Smith revealed the surface structure of lignin aggregates down to 1 angstrom -- the equivalent of a 10 billionth of a meter or smaller than the width of a carbon atom. The team's findings were published in Physical Review E.

"We've combined neutron scattering experiments with large-scale simulations on ORNL's main supercomputer to reveal that pretreated softwood lignin aggregates are characterized by a highly folded surface," said Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee.

Lignin clumps can inhibit the conversion of biofuel feedstocks -- for example, switchgrass -- into ethanol, a renewable substitute for gasoline. When enzymes are used to release plant sugars necessary for ethanol production, the lignin aggregates bind to the enzymes and reduce the efficiency of the conversion.

Lignin's highly folded surface creates more opportunities to capture the passing enzymes than a smooth surface would. An improved understanding of the lignin aggregates will aid scientists in efforts to design a more effective pretreatment process, which in turn could lower the cost of biofuels.

"Nature has evolved a very sophisticated mechanism to protect plants against enzymatic attack," said ORNL team member Loukas Petridis. "We're trying to understand the physical basis of biomass recalcitrance -- resistance of the plants to enzymatic degradation."

The complementary techniques of simulation on ORNL's Jaguar supercomputer and neutron scattering at the lab's High Flux Isotope Reactor enabled Smith's team to resolve lignin's structure at scales ranging from 1 to 1,000 angstroms. Smith's project is the first to combine the two methods in biofuel research. "This work illustrates how state-of-the-art neutron scattering and high-performance supercomputing can be integrated to reveal structures of importance to the energy biosciences," Smith said.

The research was supported by DOE's Office of Science and used the resources of the Leadership Computing Facility at ORNL under a DOE INCITE award. Team members include ORNL's Sai Venkatesh Pingali, Volker Urban, William Heller, Hugh O'Neill and Marcus Foston and Arthur Ragauskas from Georgia Institute of Technology.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by DOE/Oak Ridge National Laboratory.

Journal Reference:

Loukas Petridis, Sai Pingali, Volker Urban, William Heller, Hugh O’Neil, Marcus Foston, Arthur Ragauskas, Jeremy Smith. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Physical Review E, 2011; 83 (6) DOI: 10.1103/PhysRevE.83.061911

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here