On the formation of protein tertiary structure on a computer.

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Abstract
Computer simulation studies of some factors responsible for protein tertiary structure were performed. It is possible to obtin (fold) a compact globular conformation from a sequence of amino acids consisting of only glycines and alanines. Glycines apparently play a central role in stabilizing globular structures by facilitating the formation of turns and by destabilizing helical structures. Using this simple 2-amino-acid respresentation, which serves as a control experiment, a conformation that resembles the native structure of pancreatic trypsin inhibitor, as closely as any obtained previously in folding studies, was obtained. Careful examination reveals that the true chain topology was not reproduced here or in previous studies. The discrepancies between calculated and observed structures are probably more significant than the similarities. The implications of these results for the validity of models for protein folding, the use of pancreatic trypsin inhibitor in folding studies and the possible role of glycine in the evolution of protein structure are discussed.