It has been shown in this laboratory that the free energy change upon unfolding of small globular proteins can be predicted well from crystallographic data by using an empirical structural parametrization of the energetics. We intend to examine large ensembles of partially folded states both with native-like conformation and with artificial structure in a search for potential folding nucleation sites. Using the laboratory's structural thermodynamic algorithms to evaluate these computationally generated folding intermediates will permit us to theoretically characterize the early collapse as driven by nearest neighbor effects or by long range interactions. We will thereby expand on our view of the protein folding pathway.
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