Featured Research

from universities, journals, and other organizations

Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine

Date:
November 1, 2005
Source:
Los Alamos National Laboratory
Summary:
Researchers at Los Alamos National Laboratory have set a new world's record by performing the first million-atom computer simulation in biology. Using the "Q Machine" supercomputer, Los Alamos computer scientists have created a molecular simulation of the cell's protein-making structure, the ribosome. The project, simulating 2.64 million atoms in motion, is more than six times larger than any biological simulations performed to date.

The amino acid (green) slithers into the chemical reaction center, moving through an evolutionarily ancient corridor of the ribosome (purple). The amino acid is delivered to the reaction core by the transfer RNA molecule (yellow).
Credit: Image courtesy of Los Alamos National Laboratory

Researchers at Los Alamos National Laboratory have set a new world's record by performing the first million-atom computer simulation in biology. Using the "Q Machine" supercomputer, Los Alamos computer scientists have created a molecular simulation of the cell's protein-making structure, the ribosome. The project, simulating 2.64 million atoms in motion, is more than six times larger than any biological simulations performed to date.

The ribosome is the ancient molecular factory responsible for synthesizing proteins in all organisms. Using the new tool, the Los Alamos team led by Kevin Sanbonmatsu is the first to observe the entire ribosome in motion at atomic detail. This first simulation of the ribosome offers a new method for identifying potential antibiotic targets for such diseases as anthrax. Until now, only static, snapshot structures of the ribosome have been available.

A paper describing the effort will appear in the Proceedings of the National Academy of Sciences, Oct. 24 edition.

Sanbonmatsu posits that this technique offers a powerful new tool for understanding molecular machines and improving the efficacy of antibiotics. Antibiotic drugs are less than one one-thousandth the size of the ribosome and act like a monkey-wrench in the machinery of the cell. Such drugs diffuse into the most critical sites of this molecular machine and grind the inner working of the ribosome to a halt.

"Designing drugs based on only static structures of the ribosome might be akin to intercepting a missile knowing only the launch location and the target location with no radar information. Our simulations enable us to map out the path of the missile's trajectory," Sanbonmatsu said.

"The methods and implications lie at the interface between biochemistry, computer science, molecular biology, physics, structural biology and materials science," said Sanbonmatsu. "I believe the results serve as a proof-of-principle for materials scientists, chemists and physicists performing similar simulations of artificial molecular machines in the emerging field of nano-scale information processing.

Sanbonmatu's study focuses on decoding, the essential phase during protein synthesis within the cell wherein information transfers from RNA to protein, completing the information flow specified by Francis Crick in 1958 and known as the Central Dogma of Molecular Biology. "The ribosome is, in fact, a nano-scale computer and is very much analogous to the 'CPU' of the cell," he said.

The ribosome is so fundamental to life that many portions of this molecular machine are identical in every organism ever genetically sequenced. In developing the project, the team identified a corridor inside the ribosome that the transfer RNA must pass through for the decoding to occur, and it appears to be constructed almost entirely of universal bases, implying that it is evolutionarily ancient.

The corridor represents a new region of the ribosome containing a variety of potential new antibiotic targets. The simulations also reveal that the essential translating molecule, transfer RNA, must be flexible in two places for decoding to occur, furthering the growing belief that transfer RNA is a major player in the machine-like movement of the ribosome. The simulation also sets the stage for future biochemical research into decoding by identifying 20 universally conserved ribosomal bases important for accommodation, as well as a new structural gate, which may act as a control mechanism during transfer RNA selection.

The multi-million-atom simulation was run on 768 of the "Q" machine's 8,192 available processors. Sanbonmatsu worked to develop the simulation with Chang-Shung Tung of Los Alamos, as well as Simpson Joseph of the University of California at San Diego.

Funding for the research was provided by the National Institutes of Health, Los Alamos National Laboratory's research and development fund, and support from the Laboratory's Institutional Computing Project.

###

See an image of the Q machine at http://www.lanl.gov/asci/.


Story Source:

The above story is based on materials provided by Los Alamos National Laboratory. Note: Materials may be edited for content and length.


Cite This Page:

Los Alamos National Laboratory. "Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine." ScienceDaily. ScienceDaily, 1 November 2005. <www.sciencedaily.com/releases/2005/11/051101223046.htm>.
Los Alamos National Laboratory. (2005, November 1). Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine. ScienceDaily. Retrieved September 30, 2014 from www.sciencedaily.com/releases/2005/11/051101223046.htm
Los Alamos National Laboratory. "Largest Computational Biology Simulation Mimics Life's Most Essential Nanomachine." ScienceDaily. www.sciencedaily.com/releases/2005/11/051101223046.htm (accessed September 30, 2014).

Share This



More Plants & Animals News

Tuesday, September 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Earth Has Lost Half Its Vertebrate Wildlife Since 1970: WWF

Earth Has Lost Half Its Vertebrate Wildlife Since 1970: WWF

Newsy (Sep. 30, 2014) A new study published by the World Wide Fund for Nature found that more than half of the world's wildlife population has declined since 1970. Video provided by Newsy
Powered by NewsLook.com
California University Designs Sustainable Winery

California University Designs Sustainable Winery

Reuters - US Online Video (Sep. 27, 2014) Amid California's worst drought in decades, scientists at UC Davis design a sustainable winery that includes a water recycling system. Vanessa Johnston reports. Video provided by Reuters
Powered by NewsLook.com
Argentina Worries Over Decline of Soybean Prices

Argentina Worries Over Decline of Soybean Prices

AFP (Sep. 27, 2014) The drop in price of soy on the international market is a cause for concern in Argentina, as soybean exports are a major source of income for Latin America's third largest economy. Duration: 01:10 Video provided by AFP
Powered by NewsLook.com
Mama Bear, Cubs Hang out in California Backyard

Mama Bear, Cubs Hang out in California Backyard

Reuters - US Online Video (Sep. 27, 2014) A mama bear and her two cubs climb trees, wrestle and take naps in the backyard of a Monrovia, California home. Vanessa Johnston reports. Video provided by Reuters
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