Interacting protein theory awaits test from new neutron analysis tools

Sep 27, 2007

An international collaboration directed by an Oak Ridge National Laboratory researcher has performed the first-ever atomic-detail computer simulation of how proteins vibrate in a crystal.

Jeremy Smith, who leads ORNL's Center for Molecular Biophysics, said experimental testing of the theoretical work will require the capabilities of the Office of Science's recently completed Spallation Neutron Source at ORNL.

The study is a collaboration between Smith, who also holds a University of Tennessee-ORNL Governor's Chair, and researchers from the California Institute of Technology and the National Institute of Chemistry, Ljubljana, Slovenia. The work is published in the current issue of Physical Review Letters.

Understanding how proteins--life's worker molecules--interact with each other is a major goal of biological sciences. The simulation, which was made possible by recent advances in scientific computing, describes the forces and vibrations involved in protein crystals, which provide an environment in which the proteins are ordered and thus lend themselves to detailed study.

According to Smith, lattice dynamics describe how the repeating units of a crystal vibrate relative to each other. The resulting "phonon dispersion relations" relate the frequencies to the wavelengths of the oscillations.

Phonon dispersion relations provide information on how proteins interact with each other that could be useful for understanding protein-protein interactions in the living cell. Until now, researchers have lacked the computing power to allow atomic-detail lattice dynamical calculations.

Smith said the PRL paper predicts the existence and forms of the protein crystal lattice modes.

"In doing so it throws out a challenge to next-generation neutron science to finally make the breakthrough and determine the forms and frequencies of the vibrations experimentally," he said.

In other words, having overcome their computational hurdle, the lattice dynamics team is now ready for the SNS to test the simulation work and see if what is predicted is really there.

"Atomic-detail crystal dynamics calculations have not been possible before, and now we also have an experimental tool--the SNS--that will have the capability to test our simulations. We are looking forward to seeing the next generation of instruments at SNS demonstrate their talents." Smith said, humbly adding, "Hopefully, the calculations won't be too painfully off the mark."

Smith believes the SNS and its arsenal of specialized analytical instruments will be able to confirm--or contradict--what the simulations indicate.

"We appreciate that examining complicated proteins in this way will not be easy, even for SNS. However, with SNS instruments expected to be in some cases hundreds of times improved over currently existing facilities, we are confident that the neutron breakthrough is within reach," Smith said.

Source: Oak Ridge National Laboratory

Explore further: And so they beat on, flagella against the cantilever

add to favorites email to friend print save as pdf

Related Stories

Scientists monitoring Hawaii lava undertake risks

14 minutes ago

New photos from the U.S. Geological Survey's Hawaiian Volcano Observatory give a glimpse into the hazardous work scientists undertake to monitor lava that's threatening to cross a major highway.

Germany's Bayer says will float chemicals division

4 minutes ago

German chemicals and pharmaceuticals giant Bayer, maker of Aspirin painkiller, said on Thursday it intends to float its chemicals Material Science division to focus on its life sciences activities in human and animal health.

Facebook dressed down over 'real names' policy

8 hours ago

Facebook says it temporarily restored hundreds of deleted profiles of self-described drag queens and others, but declined to change a policy requiring account holders to use their real names rather than drag names such as ...

Recommended for you

And so they beat on, flagella against the cantilever

Sep 16, 2014

A team of researchers at Boston University and Stanford University School of Medicine has developed a new model to study the motion patterns of bacteria in real time and to determine how these motions relate ...

Tandem microwave destroys hazmat, disinfects

Sep 16, 2014

Dangerous materials can be destroyed, bacteria spores can be disinfected, and information can be collected that reveals the country of origin of radiological isotopes - all of this due to a commercial microwave ...

Cornell theorists continue the search for supersymmetry

Sep 16, 2014

(Phys.org) —It was a breakthrough with profound implications for the world as we know it: the Higgs boson, the elementary particle that gives all other particles their mass, discovered at the Large Hadron ...

How did evolution optimize circadian clocks?

Sep 12, 2014

(Phys.org) —From cyanobacteria to humans, many terrestrial species have acquired circadian rhythms that adapt to sunlight in order to increase survival rates. Studies have shown that the circadian clocks ...

User comments : 0