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 Start of work for the world's largest electric truck
20.04.2018 | Empa - Eidgenössische Materialprüfungs- und Forschungsanstalt

nachricht Tiny implants for cells are functional in vivo
19.03.2018 | Universität Basel

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

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

Im Focus: Spider silk key to new bone-fixing composite

University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.

Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.

Im Focus: Writing and deleting magnets with lasers

Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.

Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...

Im Focus: Gamma-ray flashes from plasma filaments

Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.

The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...

Im Focus: Basel researchers succeed in cultivating cartilage from stem cells

Stable joint cartilage can be produced from adult stem cells originating from bone marrow. This is made possible by inducing specific molecular processes occurring during embryonic cartilage formation, as researchers from the University and University Hospital of Basel report in the scientific journal PNAS.

Certain mesenchymal stem/stromal cells from the bone marrow of adults are considered extremely promising for skeletal tissue regeneration. These adult stem...

Im Focus: Like a wedge in a hinge

Researchers lay groundwork to tailor drugs for new targets in cancer therapy

In the fight against cancer, scientists are developing new drugs to hit tumor cells at so far unused weak points. Such a “sore spot” is the protein complex...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

IWOLIA: A conference bringing together German Industrie 4.0 and French Industrie du Futur

09.04.2018 | Event News

 
Latest News

Magnetic nano-imaging on a table top

20.04.2018 | Physics and Astronomy

Start of work for the world's largest electric truck

20.04.2018 | Interdisciplinary Research

Atoms may hum a tune from grand cosmic symphony

20.04.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>