Navigation Links
Researchers make the leap to whole-cell simulations
Date:3/30/2011

CHAMPAIGN, lll. Researchers have built a computer model of the crowded interior of a bacterial cell that in a test of its response to sugar in its environment accurately simulates the behavior of living cells.

The new "in silico cells" are the result of a collaboration between experimental scientists at the Max Planck Institute of Biology in Germany and theoretical scientists at the University of Illinois using the newest GPU (graphics processing unit) computing technology.

Their study appears in the journal PLoS Computational Biology.

"This is the first time that we're modeling entire cells with the complete contents of the cellular cytoplasm represented," said Illinois postdoctoral researcher and lead author Elijah Roberts. "We're looking at the influence of the whole cellular architecture instead of modeling just a portion of the cell, as people have done previously."

University of Illinois chemistry professor Zaida Luthey-Schulten, who led the research, had done molecular dynamics simulations of individual molecules or groups of molecules involved in information processing, but never of a system as large and complex as the interior of an entire cell.

Then in 2006 she saw a paper by Wolfgang Baumeister and his colleagues at Max Planck that located every one of a bacterium's ribosomes, its protein-building machines, inside the cell.

That image spurred Luthey-Schulten to think about modeling an entire cell, and she asked Baumeister and his colleague Julio Ortiz if they would repeat the study in Escherichia coli (E. coli), a bacterium that has been the subject of numerous molecular studies.

Once the new ribosome data were available, Roberts looked to other studies that described the size distribution of the rest of the molecules that take up space in the cell. By adding these to the ribosome data, he developed a three-dimensional model that showed the degree of "molecular crowding" in a typical E. coli cell.

Luthey-Schulten was amazed at how little "space" remained inside the cell, she said.

"I think, like everybody else, my perception of the cell up until Wolfgang and Julio's 2006 article had always been that it's a pretty big sack of water where a lot of chemical reactions occur," she said.

"But in fact there are a lot of obstacles in the cell, and that is going to affect how individual molecules move around and it's going to affect the reactions that occur."

Other researchers have begun studying the effects of molecular crowding on cellular processes, but never at the scale of an entire cell.

Those studying live cells can by conducting fluorescence experiments discover variations in the copy number of a particular protein in a population of cells. But they are less able to observe the microscopic details that give rise to such differences between genetically identical cells. Well-designed computer simulations of whole cells can track every reaction within the cells while also accounting for the influence of molecular crowding and other variations between cells, Luthey-Schulten said.

For example, by running simulations on models of two E. coli strains, the researchers were able to see that "bacterial cell architecture does indeed affect the reactions that occur within the cells," Luthey-Schulten said. When sugar was present in its environment, a longer, narrower E. coli strain was able to ramp up production of a sugar-transporter protein much more quickly than a bigger strain, the researchers found. That difference had a lot to do with the distribution of molecules in each cell type, Roberts said.

The computer simulation also showed how molecular crowding influences the behavior of a molecule that, when it binds to DNA, shuts down production of the sugar-transporter protein. Even when it wasn't bound to DNA, this repressor remained close to the binding site because other molecules in the cell blocked its escape. These intracellular obstacles reduced its ability to diffuse away.

The new model is only a first step toward an accurate simulation of a whole working cell, the researchers said. The development of better models will rely on the work of those conducting research on actual cells. Their data provide the framework for improving computer models, Luthey-Schulten said, and offer a real-world test of the in silico cells' ability to recreate the behavior of living cells.


'/>"/>

Contact: Diana Yates, Life Sciences Editor
diya@illinois.edu
217-333-5802
University of Illinois at Urbana-Champaign
Source:Eurekalert  

Related medicine news :

1. Stepchildren relate to stepparents based on perceived benefits, researchers find
2. Researchers find many elderly men are undergoing unnecessary PSA screenings
3. AACR and Landon Foundation support the next generation of researchers with INNOVATOR Awards
4. Can you hear me now? Researchers detail how neurons decide how to transmit information
5. AACR honors eminent researchers
6. Penn researchers uncover novel immune therapy for pancreatic cancer
7. Researchers: Sexually active teens need confidential health care
8. Researchers develop a halometer that tests alterations in night vision
9. ESCEO-AMGEN Fellowship awarded to Swedish and Argentinean researchers
10. Mouse Sperm Successfully Grown in Lab, Researchers Say
11. Mayo Clinic researchers find cardiac pacing helps epilepsy patients with ictal asystole
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Researchers make the leap to whole-cell simulations
(Date:4/28/2016)... ... April 28, 2016 , ... ... and Collaboration Platform™ , today announced a new Residency Education & Collaboration ... to medical knowledge, educational resources, and a host of collaboration tools designed ...
(Date:4/28/2016)... ... April 28, 2016 , ... ... been named a Top Doc in Physical Medicine and Rehabilitation by Philadelphia Magazine. ... Connolly Medical, Ltd. by randomly surveying physicians and medical leadership across the country. ...
(Date:4/28/2016)... ... April 28, 2016 , ... ... announced it will demonstrate its leading secure mobility workstation suite, SentinelSecure™, at MobileIron’s ... at Hilton Union Square, this will be MobileIron’s 6th Mobile First Conference and ...
(Date:4/28/2016)... (PRWEB) , ... April 28, 2016 , ... The ... Prevention (CDC) has established an ICD-10-CM code for sarcopenia, giving it recognition for separate ... medical community effective October 1, 2016. , Sarcopenia is defined as a combination of ...
(Date:4/28/2016)... ... April 28, 2016 , ... Boston Laser is now ... Drug Administration (FDA). The treatment consists of the application of Riboflavin, a vitamin, to ... fibers which in turn strengthens the cornea to slow the progression of keratoconus. , ...
Breaking Medicine News(10 mins):
(Date:4/27/2016)... , April 27, 2016 Tie-up ... initiative to save newborns   ... women & newborns in collaboration with Breast Milk Foundation (BMF), ... first Pasteurized Human Milk Bank, ,Amaara, in Delhi-NCR today. This ... food source for infants and should be available to babies ...
(Date:4/27/2016)... Oasmia Pharmaceutical AB (NASDAQ: ... new generation of drugs within human and veterinary ... Paclical/Apealea in the Phase III study that included ... cancer. These preliminary results showed non-inferiority between the ... versus Taxol in combination with carboplatin. In fact, ...
(Date:4/26/2016)... , April 26, 2016 Diplomat Pharmacy, Inc. ... Jennifer Hagerman , Pharm D., to Vice President ... role at Diplomat, Hagerman will continue to lead and ... that delivers custom education and training to Diplomat employees ... pharmacy industry. Diplomat University also houses the quality assurance ...
Breaking Medicine Technology: