Featured Research

from universities, journals, and other organizations

Quantum Biology: Powerful Computer Models Reveal Key Biological Mechanism

Date:
January 16, 2007
Source:
Rensselaer Polytechnic Institute
Summary:
Using powerful computers to model the intricate dance of atoms and molecules, researchers at Rensselaer Polytechnic Institute have revealed the mechanism behind an important biological reaction. In collaboration with scientists from the Wadsworth Center of the New York State Department of Health, the team is working to harness the reaction to develop a "nanoswitch" for a variety of applications, from targeted drug delivery to genomics and proteomics to sensors.

Intein crystal prior to protein splicing.
Credit: Rensselaer/Philip Shemella

Using powerful computers to model the intricate dance of atoms and molecules, researchers at Rensselaer Polytechnic Institute have revealed the mechanism behind an important biological reaction. In collaboration with scientists from the Wadsworth Center of the New York State Department of Health, the team is working to harness the reaction to develop a "nanoswitch" for a variety of applications, from targeted drug delivery to genomics and proteomics to sensors.

The research is part of a burgeoning discipline called "quantum biology," which taps the skyrocketing power of today's high-performance computers to precisely model complex biological processes. The secret is quantum mechanics -- the much-touted theory from physics that explains the inherent "weirdness" of the atomic realm.

Reporting in the February 2007 issue of Biophysical Journal, the researchers describe a mechanism to explain how an intein -- a type of protein found in single-celled organisms and bacteria -- cuts itself out of the host protein and reconnects the two remaining strands. The intein breaks a protein sequence at two points: first the N-terminal, and then the C-terminal. This aspect of the project, which is led by Saroj Nayak, associate professor of physics, applied physics, and astronomy at Rensselaer, focuses on the C-terminal reaction.

Another Rensselaer team previously found that the reaction at the C-terminal speeds up in acidic environments. But to control the reaction and use it as a nanoswitch, a better understanding of the mechanism behind this reaction is needed, according to Philip Shemella, a doctoral student in physics at Rensselaer and corresponding author of the current paper.

"You can use this protein that cuts itself and joins the pieces together in a predictable way," he said. "It already has a function that would be nice to harness for nanotechnology purposes." And because the reaction may be sensitive to light and other environmental stimuli, the process could become more than just a two-way switch between "on" and "off."

The researchers revealed the details of the reaction mechanism by applying the principles of quantum mechanics -- a mathematical framework that describes the seemingly strange behavior of the smallest known particles. For example, quantum mechanics predicts that an electron can be in two different places at the same time; or that an imaginary cat can be simultaneously dead and alive, as suggested by one famous thought experiment.

Until recently, scientists could not apply quantum mechanics to biological systems because of the large numbers of atoms involved. But the latest generation of supercomputers, along with the development of efficient mathematical tools to solve quantum mechanical equations, is making these calculations possible, according to Shemella.

"Typically, quantum mechanics has been applied to solid-state problems because the symmetry makes the calculation smaller and easier, but there's really nothing different physically between a carbon atom in a protein and a carbon atom in a nanotube," he said. "Even though a protein is such an asymmetric, complex system, when you really zoom into the quantum mechanical level, they are just atoms. It doesn't matter if strange things are happening; it's still just carbon, nitrogen, hydrogen, and oxygen."

Quantum mechanics allows researchers to do things that can't be done with classical physics, such as modeling the way chemical bonds break and form, or including the effect of proton "tunneling" -- allowing protons to move through energy barriers that normal logic would deem impossible.

For this project, the researchers used computing facilities at Rensselaer's Scientific Computation Research Center (SCOREC) and the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign. In the future, they hope to take advantage of Rensselaer's new Computational Center for Nanotechnology Innovations -- a $100 million partnership between Rensselaer, IBM, and New York state to create one of the world's most powerful university-based supercomputing centers.

The additional computing power will allow them to model complex biological systems with even greater accuracy: "The more atoms you include, the more accurate your system," Shemella said.

The paper's other authors from Rensselaer were Georges Belfort, principal investigator for the project and the Russell Sage Professor of Chemical Engineering; Shekhar Garde, the Elaine and Jack S. Parker Career Development Professor of Chemical and Biological Engineering; Brian Pereira, a graduate student in chemical engineering; and Yiming Zhang, a graduate student in physics. Patrick Van Roey, a research scientist at the Wadsworth Center, also contributed to the project.

The research was funded by a grant from the National Science Foundation to Georges Belfort at Rensselaer, and a grant from the National Institutes of Health to Marlene Belfort at the Wadsworth Center.


Story Source:

The above story is based on materials provided by Rensselaer Polytechnic Institute. Note: Materials may be edited for content and length.


Cite This Page:

Rensselaer Polytechnic Institute. "Quantum Biology: Powerful Computer Models Reveal Key Biological Mechanism." ScienceDaily. ScienceDaily, 16 January 2007. <www.sciencedaily.com/releases/2007/01/070116133617.htm>.
Rensselaer Polytechnic Institute. (2007, January 16). Quantum Biology: Powerful Computer Models Reveal Key Biological Mechanism. ScienceDaily. Retrieved April 24, 2014 from www.sciencedaily.com/releases/2007/01/070116133617.htm
Rensselaer Polytechnic Institute. "Quantum Biology: Powerful Computer Models Reveal Key Biological Mechanism." ScienceDaily. www.sciencedaily.com/releases/2007/01/070116133617.htm (accessed April 24, 2014).

Share This



More Matter & Energy News

Thursday, April 24, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

UN Joint Mission Starts Removing Landmines in Cyprus

UN Joint Mission Starts Removing Landmines in Cyprus

AFP (Apr. 23, 2014) The UN mission in Cyprus (UNFICYP) led a mine clearance demonstration on Wednesday in the UN-controlled buffer zone where demining operations are being conducted near the Cypriot village of Mammari. Duration: 01:00 Video provided by AFP
Powered by NewsLook.com
Air Force: $4.2B Saved from Grounding A-10s

Air Force: $4.2B Saved from Grounding A-10s

AP (Apr. 23, 2014) Speaking about the future of the United States Air Force, Chief of Staff Gen. Mark Welsh says the choice to divest the A-10 fleet was logical and least impactful. (April 23) Video provided by AP
Powered by NewsLook.com
Jets Fuel Jump in Boeing's Revenue

Jets Fuel Jump in Boeing's Revenue

Reuters - Business Video Online (Apr. 23, 2014) A sharp rise in revenue for commercial jets offset a decline in Boeing's defense business. And a big increase in deliveries lifted profitability. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com
Is North Korea Planning Nuclear Test #4?

Is North Korea Planning Nuclear Test #4?

Newsy (Apr. 22, 2014) South Korean officials say North Korea is preparing to conduct another nuclear test, but is Pyongyang just bluffing this time? 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:
from the past week

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