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 Bergamotene - alluring and lethal for Manduca sexta
21.04.2017 | Max-Planck-Institut für chemische Ökologie

nachricht How to color a lizard: From biology to mathematics
13.04.2017 | Université de Genève

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

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

Im Focus: Manipulating Electron Spins Without Loss of Information

Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.

For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...

Im Focus: The proton precisely weighted

What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.

To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...

Im Focus: On the way to a biological alternative

A bacterial enzyme enables reactions that open up alternatives to key industrial chemical processes

The research team of Prof. Dr. Oliver Einsle at the University of Freiburg's Institute of Biochemistry has long been exploring the functioning of nitrogenase....

Im Focus: The 1 trillion tonne iceberg

Larsen C Ice Shelf rift finally breaks through

A one trillion tonne iceberg - one of the biggest ever recorded -- has calved away from the Larsen C Ice Shelf in Antarctica, after a rift in the ice,...

Im Focus: Laser-cooled ions contribute to better understanding of friction

Physics supports biology: Researchers from PTB have developed a model system to investigate friction phenomena with atomic precision

Friction: what you want from car brakes, otherwise rather a nuisance. In any case, it is useful to know as precisely as possible how friction phenomena arise –...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

»We are bringing Additive Manufacturing to SMEs«

19.07.2017 | Event News

The technology with a feel for feelings

12.07.2017 | Event News

Leipzig HTP-Forum discusses "hydrothermal processes" as a key technology for a biobased economy

12.07.2017 | Event News

 
Latest News

Researchers create new technique for manipulating polarization of terahertz radiation

20.07.2017 | Information Technology

High-tech sensing illuminates concrete stress testing

20.07.2017 | Materials Sciences

First direct observation and measurement of ultra-fast moving vortices in superconductors

20.07.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>