Featured Research

from universities, journals, and other organizations

Powerful supercomputer peers into the origin of life

Date:
October 4, 2010
Source:
DOE/Oak Ridge National Laboratory
Summary:
Supercomputer simulations are helping scientists unravel how nucleic acids could have contributed to the origins of life.

New research at Oak Ridge National Laboratory explains how a ribonucleic acid enzyme, or ribozyme (pictured), uses magnesium ions (seen as spheres) to accelerate a significant reaction in organic chemistry.
Credit: Image courtesy of DOE/Oak Ridge National Laboratory

Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life.

Related Articles


A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms.

Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions -- two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.

"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."

The research team found a theoretical explanation for why the Diels-Alder ribozyme needs magnesium to function. Computational models of the ribozyme's internal motions allowed the researchers to capture and understand the finer details of the fast-paced reaction. The static nature of conventional experimental techniques such as chemical probing and X-ray analysis had not been able to reveal the dynamics of the system.

"Computer simulations can provide insight into biological systems that you can't get any other way," Smith said. "Since these structures are changing so much, the dynamic aspects are difficult to understand, but simulation is a good way of doing it."

Smith explained how their calculations showed that the ribozyme's internal dynamics included an active site, or "mouth," which opens and closes to control the reaction. The concentration of magnesium ions directly impacts the ribozyme's movements.

"When there's no magnesium present, the mouth closes, the substrate can't get in, and the reaction can't take place. We found that magnesium ions bind to a special location on the ribozyme to keep the mouth open," Smith said.

The research was published as "Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme" in the Journal of the American Chemical Society. The research team included Tomasz Berezniak and Mai Zahran, who are Smith's graduate students, and Petra Imhof and Andres Jδschke from the University of Heidelberg.

Smith's research was supported by Laboratory Directed Research and Development program funding. The bulk of the simulations were performed on the Kraken supercomputer at the UT/ORNL National Institute for Computational Sciences, supported by a National Science Foundation Teragrid allocation, and the resulting data were analyzed on the Heidelberg Linux Cluster System at the Interdisciplinary Center for Scientific Computing of the University of Heidelberg.


Story Source:

The above story is based on materials provided by DOE/Oak Ridge National Laboratory. Note: Materials may be edited for content and length.


Cite This Page:

DOE/Oak Ridge National Laboratory. "Powerful supercomputer peers into the origin of life." ScienceDaily. ScienceDaily, 4 October 2010. <www.sciencedaily.com/releases/2010/10/101004151725.htm>.
DOE/Oak Ridge National Laboratory. (2010, October 4). Powerful supercomputer peers into the origin of life. ScienceDaily. Retrieved November 29, 2014 from www.sciencedaily.com/releases/2010/10/101004151725.htm
DOE/Oak Ridge National Laboratory. "Powerful supercomputer peers into the origin of life." ScienceDaily. www.sciencedaily.com/releases/2010/10/101004151725.htm (accessed November 29, 2014).

Share This


More From ScienceDaily



More Fossils & Ruins News

Saturday, November 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

New Dinosaur Species Found in Museum Collection

New Dinosaur Species Found in Museum Collection

Reuters - Innovations Video Online (Nov. 27, 2014) — A British palaeontologist has discovered a new species of dinosaur while studying fossils in a Canadian museum. Pentaceratops aquilonius was related to Triceratops and lived at the end of the Cretaceous Period, around 75 million years ago. Jim Drury has more. Video provided by Reuters
Powered by NewsLook.com
Classic Hollywood Memorabilia Goes Under the Hammer

Classic Hollywood Memorabilia Goes Under the Hammer

Reuters - Entertainment Video Online (Nov. 26, 2014) — The iconic piano from "Casablanca" and the Cowardly Lion suit from "The Wizard of Oz" fetch millions at auction. Sara Hemrajani reports. Video provided by Reuters
Powered by NewsLook.com
3D Map of Antarctic Sea Ice to Shed Light on Climate Change

3D Map of Antarctic Sea Ice to Shed Light on Climate Change

Reuters - Innovations Video Online (Nov. 24, 2014) — A multinational group of scientists have released the first ever detailed, high-resolution 3-D maps of Antarctic sea ice. Using an underwater robot equipped with sonar, the researchers mapped the underside of a massive area of sea ice to gauge the impact of climate change. Ben Gruber reports. Video provided by Reuters
Powered by NewsLook.com
Ruins Thought To Be Port Actually Buried Greek City

Ruins Thought To Be Port Actually Buried Greek City

Newsy (Nov. 24, 2014) — Media is calling it an "underwater Pompeii." Researchers have found ruins off the coast of Delos. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins