Kinetic simulations of the folding and unfolding of the mammalian TIM barrel protein aldolase were conducted to determine if a minimalist monomeric Gō model, using the native structure to determine attractive energies in the protein chain, could capture the experimentally determined folding pathway. The folding order, that is, the order in which different secondary structures fold, between the Gō model simulations and that from hydrogen-deuterium exchange experiments, did not agree. To explain this discrepancy, two alternate variant of the basic Gō model were simulated: (1) a monomer Gō model with native contact energies weighted by a statistical potential (SP model) and (2) a monomer Gō model with native contact energies inversely weighted by crystallographic B factors (B model).
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