Model Polymers Reveal New Clues to Protein Folding

e that depends upon the energy of the bonds that form when the acid residues come close together, and upon whether a given group of amino acid residues is hydrophobic or hydrophilic, and so on. But newly manufactured proteins are far from their native state.

Proteins are punched out rather like ticker-tape by ribosomes that add amino acids one at a time. Although the order of the amino acids is ultimately specified by a length of DNA (the gene for that protein), how the order specifies the protein's distinctively folded structure and directs pathways to that structure is not yet understood.

"Protein chains all fold differently-even proteins of the same kind fold into their final state by sampling many different conformations-because they start from different initial states," says Rokhsar. "Yet somehow they start from an unfolded state and achieve the folded structure quickly, reliably, and reversibly."

To demonstrate the magnitude of the challenge, Rokhsar suggests contemplating a single node-a stand-in for a single amino acid residue-represented by a ball on the end of a stick. "Let's limit to five the directions the next stick-and-ball can extend-right, left, up, down, or straight ahead," says Rokhsar. "If there are five links in the chain, that's five to the fifth ways the chain could fold, 3,125 possibilities. If there are a hundred links in the chain-not unusual for a protein-there would be something like 10 to the 30th possibilities. If you tried them randomly, even a trillion times a second, it would take longer than the age of the universe to get the right structure."

Rokhsar and Pande, who is a Miller Postdoctoral Fellow at UC Berkeley's Department of Physics, approached the problem by designing a protein-like model heteropolymer of 48 units whose properties define a stable "native structure"-a compact lattice in three dimensions with each bend at a right angle, resembling a jungle gym made of Tinker Toys.

Using the Cray T3E compute

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

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