Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Study Shows Factors Affecting Molecule Motion in Cells

12.10.2010
Using large-scale computer simulations, researchers at the Georgia Institute of Technology have identified the most important factors affecting how molecules move through the crowded environment inside living cells.

The findings suggest that perturbations caused by hydrodynamic interactions – similar to what happens when the wake from a large boat affects smaller boats on a lake – may be the most important factor in this intracellular diffusion.

A detailed understanding of the interactions inside cells – where macromolecules can occupy as much as 40 percent of the available space – could provide important information to the developers of therapeutic drugs and lead to a better understanding of how disease states develop. Ultimately, researchers hope to have a complete simulation of these cellular processes to help them understand a range of biological issues, from metabolism to cell division.

Sponsored by the National Institutes of Health, the research was reported Oct. 11 in the early online edition of the journal Proceedings of the National Academy of Sciences.

“We found that hydrodynamics – perturbation of the solvent with eddies and wakes created by molecules in this crowded environment – may be the dominant effect in intermolecular dynamics within cells,” said Jeffrey Skolnick, director of the Center for the Study of Systems Biology at Georgia Tech. “The correlations created between molecules through this process have a lot of functional consequences for how collections of these molecules interact.”

The motion of macromolecules within cells is normally random, occurring through Brownian motion that causes the molecules to diffuse through the cellular cytoplasm, which has viscosity similar to that of water. Researchers have studied the movement of fluorescent protein molecules injected into E. coli cells, but don’t yet understand the forces affecting that motion. However, the measurements show that the fluorescent molecules move about 15 times more slowly inside the cell than they do in a test tube.

Using simulations that allowed them to adjust the impacts of natural forces, Skolnick and collaborator Tadashi Ando analyzed the activity of 15 different molecules in a portion – just one one-thousandth – of an E. coli cell. By altering those simulated forces in the computer, they attempted to determine what may cause the reduction in diffusion speed.

The most logical reason for that slowed movement is the crowded nature of cells, but Skolnick and Ando found that bumping into other molecules accounted for only a portion of the reduced molecular diffusion.

“If you are in a crowded room and want to walk to the bar, the other people slow you down,” explained Skolnick, who is Georgia Research Alliance eminent scholar in computational systems biology. “In biological processes, if there are a lot of large molecules in the way, these protein molecules can’t move as quickly. But our model showed that this crowding accounted for only about a third of the reduction measured experimentally.”

The researchers also studied the hydrodynamic forces exerted by molecules on one another. These forces are comparable to the way in which the wake of a large boat on a lake affects smaller boats, or how a swimming whale might effect a school of small fish. The interaction causes correlated motion, which was known to be important in the movement of polymers and colloids studied earlier by chemists.

By turning off the other forces at work in their silicon world, the Georgia Tech researchers found that this correlated motion accounted for much more of the diffusion reduction than did the crowding.

“The hydrodynamic interactions create cooperative motion between the molecules,” Skolnick explained. “We see long-lived correlations between the molecules, independent of size, in space and time. This suggests that these correlated motions may be extremely important in the dynamics of molecules.”

The researchers also studied other possible causes for the slow-down but found that repulsion between molecules, variations in molecular shape and “stickiness” between molecules could not account for the dramatic reduction in diffusion rate.

Though the findings are interesting in themselves, their real importance may be in setting the stage for larger studies that would include the thousands of molecules known to be important to cellular operations. Researchers ultimately hope to model everything happening in the cell, including interactions with the cell membrane.

“This is the beginning of what will be a very complicated effort to develop the tools and approaches that will allow us to simulate a sufficiently useful caricature of a cell,” Skolnick said. “From that, we will be able to learn the biological principles at work, and then study some ‘what if’ scenarios.”

Those “what if” questions might one day help drug designers better understand how therapeutic compounds work within cells, for instance, or allow cancer researchers to see how cells change from a healthy state to a disease state.

“It would be great if we could study new drugs in a model set of cells to very quickly see what might be the side-effects and cross interactions to understand how we might minimize these problems,” Skolnick noted. “The nice thing about a computer simulation is that if it is a reasonably faithful caricature, you can ask a lot of questions – and get answers that help you understand what’s going on.”

Research News & Publications Office
Georgia Institute of Technology
75 Fifth Street, N.W., Suite 314
Atlanta, Georgia 30308 USA
Media Relations Contacts: John Toon (404-894-6986)(jtoon@gatech.edu) or Abby Vogel Robinson (abby@innovate.gatech.edu).

Technical Contact: Jeffrey Skolnick (404-407-8975)(skolnick@gatech.edu).

Writer: John Toon

John Toon | Newswise Science News
Further information:
http://www.gatech.edu

More articles from Studies and Analyses:

nachricht Drone vs. truck deliveries: Which create less carbon pollution?
31.05.2017 | University of Washington

nachricht New study: How does Europe become a leading player for software and IT services?
03.04.2017 | Fraunhofer-Institut für System- und Innovationsforschung (ISI)

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Making Waves

Computer scientists use wave packet theory to develop realistic, detailed water wave simulations in real time. Their results will be presented at this year’s SIGGRAPH conference.

Think about the last time you were at a lake, river, or the ocean. Remember the ripples of the water, the waves crashing against the rocks, the wake following...

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Nanostructures taste the rainbow

29.06.2017 | Physics and Astronomy

New technique unveils 'matrix' inside tissues and tumors

29.06.2017 | Life Sciences

Cystic fibrosis alters the structure of mucus in airways

29.06.2017 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>