Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Protein folding physics modeled at the atomic level

16.10.2002



Researchers at Los Alamos National Laboratory and the University of California, San Diego, have created the first computer simulation of full-system protein folding thermodynamics at the atomic-level. Understanding the basic physics of protein folding could solve one of the grand mysteries of computational biology.

Proteins are the basic building blocks of life and protein folding, the process by which proteins reconfigure themselves - the actions that result in structural change - are the foundation of cellular growth and the health of a biological system. When proteins incorrectly fold the malfunction can give rise to a variety of diseases. The fact that proteins fold has been known since the 1960s, but an understanding of the chemical and physical properties of folding continues to elude scientists.

Understanding how proteins undergo the folding process has largely been studied from a biologist’s point of view, probing actual proteins and studying them with high-powered microscopy techniques. Now, Los Alamos theoretical biophysicist Angel Garcia, along with colleague Jose N. Onuchic of UC San Diego, have created a computer model of protein folding that focuses on the physics of the protein folding, specifically looking at the temperature changes that occur in the process.



Findings were presented at the Rocky Mountain regional meeting of the American Chemical Society, Albuquerque.

Protein complexes can be very large molecules containing millions of atoms, and protein folding is chemically and physically complex. Folding occurs very rapidly as well, with small protein molecules folding in millionths of seconds.

"We have chosen to first look at a comparatively simple protein in water system consisting of about 18,000 atoms, called a 3-heilx bundle, that folds in a fairly simple way and relatively slowly, in about 10 microseconds," said Garcia. "Our calculation is based on Onuchic’s ’funneling theory’ of protein folding that looks at the ’energy landscape’ of folding and finds that as the protein gets closer and closer to it’s folded state it’s energy gets lower and lower."

Garcia implemented an algorithm that relies on exhaustive sampling of protein configurations and utilizes massively parallel computing combined with molecular dynamics and a random-sampling Monte Carlo simulation of the thermodynamics. The result is a computer model of the basic physical properties in a simple system that, if correct, should be applicable to even the most complex proteins. "In principle," said Garcia, "it should work for all proteins."

The protein folding problem is complex computationally because a protein can adopt many shapes and configurations that grow exponentially based on the number of amino acids in a chain, called a polypeptide. A typical protein has between 60 and 150 amino acids. A typical amino acid, like glutamine, consists of 20 carbon, hydrogen, oxygen and nitrogen atoms.

Garcia’s 18,000-atom computation was completed on 82 parallel processors over about a six-month time frame, translating to more than 34 years of Central Processing Unit time.

Garcia plans to continue working on protein folding physics, creating more complex models that mimic the physics beyond the thermodynamic, with the eventual goal of better understanding the folding process for even the most complex protein structures.


###
Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration (NNSA) of the U.S. Department of Energy and works in partnership with NNSA’s Sandia and Lawrence Livermore national laboratories to support NNSA in its mission.

Los Alamos enhances global security by ensuring the safety and reliability of the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction, and solving problems related to energy, environment, infrastructure, health and national security concerns.

Kevin Roark | EurekAlert!
Further information:
http://www.lanl.gov.

More articles from Interdisciplinary Research:

nachricht Body Talk: A New Crowdshaping Technology Uses Words to Create Accurate 3D Body Models
27.07.2016 | Max-Planck-Institut für Intelligente Systeme

nachricht When the Brain Grows, the IQ Rises
16.02.2016 | Technische Universität Chemnitz

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

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

Im Focus: OLED microdisplays in data glasses for improved human-machine interaction

The Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP has been developing various applications for OLED microdisplays based on organic semiconductors. By integrating the capabilities of an image sensor directly into the microdisplay, eye movements can be recorded by the smart glasses and utilized for guidance and control functions, as one example. The new design will be debuted at Augmented World Expo Europe (AWE) in Berlin at Booth B25, October 18th – 19th.

“Augmented-reality” and “wearables” have become terms we encounter almost daily. Both can make daily life a little simpler and provide valuable assistance for...

Im Focus: Artificial Intelligence Helps in the Discovery of New Materials

With the help of artificial intelligence, chemists from the University of Basel in Switzerland have computed the characteristics of about two million crystals made up of four chemical elements. The researchers were able to identify 90 previously unknown thermodynamically stable crystals that can be regarded as new materials. They report on their findings in the scientific journal Physical Review Letters.

Elpasolite is a glassy, transparent, shiny and soft mineral with a cubic crystal structure. First discovered in El Paso County (Colorado, USA), it can also be...

Im Focus: Complex hardmetal tools out of the 3D printer

For the first time, Fraunhofer IKTS shows additively manufactured hardmetal tools at WorldPM 2016 in Hamburg. Mechanical, chemical as well as a high heat resistance and extreme hardness are required from tools that are used in mechanical and automotive engineering or in plastics and building materials industry. Researchers at the Fraunhofer Institute for Ceramic Technologies and Systems IKTS in Dresden managed the production of complex hardmetal tools via 3D printing in a quality that are in no way inferior to conventionally produced high-performance tools.

Fraunhofer IKTS counts decades of proven expertise in the development of hardmetals. To date, reliable cutting, drilling, pressing and stamping tools made of...

Im Focus: Launch of New Industry Working Group for Process Control in Laser Material Processing

At AKL’16, the International Laser Technology Congress held in May this year, interest in the topic of process control was greater than expected. Appropriately, the event was also used to launch the Industry Working Group for Process Control in Laser Material Processing. The group provides a forum for representatives from industry and research to initiate pre-competitive projects and discuss issues such as standards, potential cost savings and feasibility.

In the age of industry 4.0, laser technology is firmly established within manufacturing. A wide variety of laser techniques – from USP ablation and additive...

Im Focus: New laser joining technologies at ‘K 2016’ trade fair

Every three years, the plastics industry gathers at K, the international trade fair for plastics and rubber in Düsseldorf. The Fraunhofer Institute for Laser Technology ILT will also be attending again and presenting many innovative technologies, such as for joining plastics and metals using ultrashort pulse lasers. From October 19 to 26, you can find the Fraunhofer ILT at the joint Fraunhofer booth SC01 in Hall 7.

K is the world’s largest trade fair for the plastics and rubber industry. As in previous years, the organizers are expecting 3,000 exhibitors and more than...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Experts from industry and academia discuss the future mobile telecommunications standard 5G

23.09.2016 | Event News

ICPE in Graz for the seventh time

20.09.2016 | Event News

Using mathematical models to understand our brain

16.09.2016 | Event News

 
Latest News

Stronger turbine blades with molybdenum silicides

26.09.2016 | Materials Sciences

Scientists Find Twisting 3-D Raceway for Electrons in Nanoscale Crystal Slices

26.09.2016 | Materials Sciences

Lowering the Heat Makes New Materials Possible While Saving Energy

26.09.2016 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>