Model Polymers Reveal New Clues to Protein Folding

r at NERSC, Rokhsar and Pande repeatedly unfolded the model by raising its (simulated) temperature, then lowered the temperature and watched it refold itself. For each folding sequence they separately tracked the position of each of the 48 "mers," the units equivalent to a protein's amino acid residues.

Even with a model far less complex than most real proteins, the number of possible initial conformations is astronomically large, and each path to stability is virtually unique. By sampling the state of the writhing polymer every 6,000 iterations-taking a single-frame snapshot of the shape-the researchers made movies that showed the model polymer seeking and eventually finding its stable state. Typically some three-quarters of a million iterations were required before the model polymer stabilized.

The average position change of each unit was recorded from frame to frame, and the rate of change was color-coded-from yellow for units that thrashed continually, through the spectrum to blue for those that held still, at least temporarily. This data could be arranged in "fluctuation smears" to give a cumulative picture of the position of the units at any moment in the process.

Remarkably, Rokhsar and Pande discovered common features among the numerous folding pathways. At first the unfolded polymers fluctuated wildly through several hundred thousand configurations-then suddenly settled into a partially folded intermediate state, in which a stable core structure was accompanied by flailing loops and dangling ends. After another couple of hundred thousand iterations, the polymer abruptly locked into its native state.

These sudden transitions are evocative of phase changes, like the changes from a gas to a liquid to a solid. There are distinct classes of intermediate states for the model polymer, however, which correspond to different groups of units that temporarily achieve stability during the intermediate phase. Each class of intermediate states represe

Contact: Paul Preuss
(510) 486-6249
DOE/Lawrence Berkeley National Laboratory

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