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.

Studying Metabolic Regulation Through Cellular Properties

Predictive models indicate cells regulate enzyme activity to maintain liquid center

The Science

Cellular metabolism is the series of chemical reactions that maintain life in living things. During this process, substances called enzymes break down and build fats, proteins, energy carriers, and genetic information. These processes happen through a complex, interconnected network of reactions. Until now, studies to identify specific reactions that regulate the overall flow through a network were too complex to do regularly. Now scientists have developed new methods that combine cutting-edge techniques to predict which enzymes control common biochemical pathways. Previously, scientists believed that the reactions that regulate flow through the network make other reactions less intense. The new study found instead that these regulating reactions actually make other reactions more intense.

The Impact

Scientists must understand how cells regulate and control themselves to continue their advances in important research areas. This knowledge will help researchers understand the fundamental science of biology. It will also help researchers design new organisms for specific purposes and develop new strategies to target and control diseases. With this new research, scientists have shown a way to identify points of metabolic regulation easily and rapidly.

Summary

Cells produce small molecules called metabolites during their regular biochemical functions. As the molecules accumulate in a cell, the inner liquid becomes thick and glassy. This makes it difficult for metabolites and biomolecules to diffuse through a cell to their target such that regulation to control these metabolites is required. However, researchers have previously faced challenges in using experiments or simulations to decipher the principles behind how cells regulate enzymatic reactions to control metabolite concentrations.

Scientists developed new methods to predict which enzymes in biochemical pathways regulate metabolite flow through organized network reactions. First, they reformulated mass action kinetics to determine reasonable rate parameters. Then, the scientists used a combination of statistical thermodynamics, control theory, and reinforcement learning (a type of machine learning) to predict which enzymes needed to be controlled to match physiological levels of metabolite concentrations. They found that metabolic regulation acts to restrict flow at the regulated reactions, pushing them further away from equilibrium. Their results also supported an often-overlooked organizational principle of biology proposed a century ago: the minimal amount of regulation needed corresponded to the maximization of entropy production.

Funding

This project was supported by the Department of Energy (DOE) Office of Science Graduate Student Research award, funding from the DOE Office of Science, Biological and Environmental Research program, the National Institute of Biomedical Imaging and Bioengineering, and the National Science Foundation.

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Newswise: Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Released: 17-May-2021 11:40 AM EDT
Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Argonne National Laboratory

Argonne senior chemist Robert Tranter, a shockwave chemist, was named a fellow of the Combustion Institute.

Newswise:Video Embedded successful-start-of-dark-energy-spectroscopic-instrument-desi-follows-record-setting-trial-run
VIDEO
Released: 17-May-2021 9:00 AM EDT
Successful Start of Dark Energy Spectroscopic Instrument (DESI) Follows Record-Setting Trial Run
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Released: 14-May-2021 5:20 PM EDT
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Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
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To understand the effects of expanding biofuel production, scientists must accurately represent biofuel crops in land surface models. Using observations from biofuel plants in the Midwestern United States, researchers simulated two biofuel perennial plants, miscanthus and switchgrass. The simulations indicate these high-yield perennial crops have several advantages over traditional annual bioenergy crops—they assimilate more carbon dioxide, and they require fewer nutrients and less water.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Department of Energy, Office of Science

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Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

View More
Newswise: Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Released: 17-May-2021 11:40 AM EDT
Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Argonne National Laboratory

Argonne senior chemist Robert Tranter, a shockwave chemist, was named a fellow of the Combustion Institute.

Newswise:Video Embedded successful-start-of-dark-energy-spectroscopic-instrument-desi-follows-record-setting-trial-run
VIDEO
Released: 17-May-2021 9:00 AM EDT
Successful Start of Dark Energy Spectroscopic Instrument (DESI) Follows Record-Setting Trial Run
Lawrence Berkeley National Laboratory

A five-year quest to map the universe and unravel the mysteries of “dark energy” is beginning officially today, May 17, at Kitt Peak National Observatory near Tucson, Arizona. To complete its quest, the Dark Energy Spectroscopic Instrument (DESI) will capture and study the light from tens of millions of galaxies and other distant objects in the universe.

Newswise: Recycling Gives New Purpose to Spent Nuclear Fuel
Released: 14-May-2021 5:20 PM EDT
Recycling Gives New Purpose to Spent Nuclear Fuel
Pacific Northwest National Laboratory

PNNL researchers developed an innovative capability to rapidly separate, monitor, and tightly control specific uranium and plutonium ratios in real-time—an important achievement in efficiently controlling the resulting product and safeguarding nuclear material.

Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Department of Energy, Office of Science

To understand the effects of expanding biofuel production, scientists must accurately represent biofuel crops in land surface models. Using observations from biofuel plants in the Midwestern United States, researchers simulated two biofuel perennial plants, miscanthus and switchgrass. The simulations indicate these high-yield perennial crops have several advantages over traditional annual bioenergy crops—they assimilate more carbon dioxide, and they require fewer nutrients and less water.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Department of Energy, Office of Science

To understand the effects of expanding biofuel production, scientists must accurately represent biofuel crops in land surface models. Using observations from biofuel plants in the Midwestern United States, researchers simulated two biofuel perennial plants, miscanthus and switchgrass. The simulations indicate these high-yield perennial crops have several advantages over traditional annual bioenergy crops—they assimilate more carbon dioxide, and they require fewer nutrients and less water.

Newswise: Harvesting Light Like Nature Does
Released: 14-May-2021 2:55 PM EDT
Harvesting Light Like Nature Does
Pacific Northwest National Laboratory

A new class of bio-inspired two-dimensional (2D) hybrid nanomaterials mimic the ability of photosynthetic plants and bacteria.

Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

View More
Newswise: Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Released: 17-May-2021 11:40 AM EDT
Argonne senior chemist Robert Tranter named fellow of the Combustion Institute
Argonne National Laboratory

Argonne senior chemist Robert Tranter, a shockwave chemist, was named a fellow of the Combustion Institute.

Newswise:Video Embedded successful-start-of-dark-energy-spectroscopic-instrument-desi-follows-record-setting-trial-run
VIDEO
Released: 17-May-2021 9:00 AM EDT
Successful Start of Dark Energy Spectroscopic Instrument (DESI) Follows Record-Setting Trial Run
Lawrence Berkeley National Laboratory

A five-year quest to map the universe and unravel the mysteries of “dark energy” is beginning officially today, May 17, at Kitt Peak National Observatory near Tucson, Arizona. To complete its quest, the Dark Energy Spectroscopic Instrument (DESI) will capture and study the light from tens of millions of galaxies and other distant objects in the universe.

Newswise: Recycling Gives New Purpose to Spent Nuclear Fuel
Released: 14-May-2021 5:20 PM EDT
Recycling Gives New Purpose to Spent Nuclear Fuel
Pacific Northwest National Laboratory

PNNL researchers developed an innovative capability to rapidly separate, monitor, and tightly control specific uranium and plutonium ratios in real-time—an important achievement in efficiently controlling the resulting product and safeguarding nuclear material.

Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Released: 14-May-2021 4:05 PM EDT
Not Just Disturbance: Turbulence Protects Fusion Reactor Walls
Department of Energy, Office of Science

To operate successfully, ITER and future fusion energy reactors cannot allow melting of the walls of the divertor plates that remove excess heat from the plasma in a reactor. These walls are especially at risk of melting when heat is applied to narrow areas. Now, however, an extreme-scale computing analysis indicates that turbulence will reduce that risk.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Department of Energy, Office of Science

To understand the effects of expanding biofuel production, scientists must accurately represent biofuel crops in land surface models. Using observations from biofuel plants in the Midwestern United States, researchers simulated two biofuel perennial plants, miscanthus and switchgrass. The simulations indicate these high-yield perennial crops have several advantages over traditional annual bioenergy crops—they assimilate more carbon dioxide, and they require fewer nutrients and less water.

Newswise: Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Released: 14-May-2021 3:35 PM EDT
Enhancing Land Surface Models to Grow Perennial Bioenergy Crops
Department of Energy, Office of Science

To understand the effects of expanding biofuel production, scientists must accurately represent biofuel crops in land surface models. Using observations from biofuel plants in the Midwestern United States, researchers simulated two biofuel perennial plants, miscanthus and switchgrass. The simulations indicate these high-yield perennial crops have several advantages over traditional annual bioenergy crops—they assimilate more carbon dioxide, and they require fewer nutrients and less water.

Newswise: Harvesting Light Like Nature Does
Released: 14-May-2021 2:55 PM EDT
Harvesting Light Like Nature Does
Pacific Northwest National Laboratory

A new class of bio-inspired two-dimensional (2D) hybrid nanomaterials mimic the ability of photosynthetic plants and bacteria.

Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

Newswise: 050721-ber-earths-atomosphere.jpg?itok=-W-tcpvH
Released: 14-May-2021 2:50 PM EDT
Scientists Check the Math for Improved Models of Liquids and Gases in Earth’s Atmosphere
Department of Energy, Office of Science

Discretization is the process of converting continuous models and variables, such as wind speed, into discrete versions to make equations that are compatible with computer analysis. Energy consistent discretization ensures that the method does not have any inaccurate sources of energy that can lead to unstable and unrealistic simulations. In this research, scientists provided a discretization for equations used by global models of the Earth’s atmosphere.

View More

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