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Proteins serve as models for understanding complex physical systems

DOE/Los Alamos National Laboratory : 23 January, 2001  (Technical Article)
People have described the 20th Century as the century of physics and claim the 21st Century will be the century of biology. It's fitting, then, that at the meeting of the American Association for the Advancement of Science one of the presentations discusses a bridge between biology and physics: using proteins and other biomolecules as models for studying complex physical systems.
'The next century may indeed be the century of biology, but physics can contribute in a major way,' said Hans Frauenfelder of the U.S. Department of Energy's Los Alamos National Laboratory.

'Proteins are some of the simplest biological systems, but they are far more complex than the systems used in physics,' Frauenfelder said. 'The idea researchers in this field have been pursuing is to use proteins as model systems for identifying the underlying laws of complexity. At the same time, we learn more about protein functions that feeds back into biology.'

Individual protein molecules can assemble themselves in a variety of different conformations, a range of shapes governed by interactions among the atoms that make up the protein; this folding process influences the proteins' functionality.

Each conformation represents a different energy level; likewise, it requires energy to shift from one conformation to another.

Over the past two decades, researchers have advanced the concept of an 'energy landscape' to describe the relation between the various conformational states. When these energy states are plotted the resulting graphic resembles the topography of a mountainous area, but in a high-dimensional space. The valleys represent the available states and the peaks the barriers between them.

'The energy landscape is an important concept that is slowly getting people's attention,' Frauenfelder said. 'When a protein folds there are a number of different but related structures it can assume. This is implied by the energy landscape, which shows there are a number of similar configurations with very similar energies.' Above a certain temperature, the protein can basically skip between different valleys in the energy landscape, changing shape and permitting functionality.

The existence of various states of nearly identical energies means a protein can change shape to enable it to interact with other molecules. If there were a single lowest-energy state, the protein would be stuck in that one conformation, would be rigid and wouldn't be able to perform its function.

The other notion researchers have advanced is that the energy landscape is organized in a hierarchical way: within each valley there are dips and wiggles, and within those still more, an increasingly fine detail built into the landscape.

Researchers now are applying the ideas of an energy landscape with a hierarchical structure, gained from studying proteins, to complex, macroscopic systems. Frauenfelder points to 'spin glasses' as materials that can exist in a large number of similar but different structures. One example of a spin glass is a dilute alloy of iron in gold. The interactions of the iron atoms in the alloy lead to different bulk states similar to a protein's many conformational states.

Looking at spin glasses from an energy landscape perspective has gained physicist's fresh insights into the behavior of these materials.

Frauenfelder said to exploit these ideas fully, there needs to be continuous exchange of information among physics, biology and chemistry. He noted that the national laboratories are ideally suited for driving this interdisciplinary science.
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