IDENTIFICATION OF COOPERATIVE FOLDING UNITS IN A SET OF NATIVE PROTEINS

Cooperative unfolding penalties are calculated by statistically evalua ting an ensemble of denatured states derived from native structures. T he ensemble of denatured states is determined by dividing the native p rotein into short contiguous segments and defining all possible combin ations of native, i.e., interacting, and non-native, i.e., non-interac ting, segments. We use a novel knowledge-based scoring function, deriv ed from a set of non-homologous proteins in the Protein Data Bank, to describe the interactions among residues. This procedure is used for t he structural identification of cooperative folding cores for four glo bular proteins: bovine pancreatic trypsin inhibitor, horse heart cytoc hrome c, French bean plastocyanin, and staphylococcal nuclease. The th eoretical folding units are shown to correspond to regions that exhibi t enhanced stability against denaturation as determined from experimen tal hydrogen exchange protection factors. Using a sequence similarity score for related sequences, we show that, in addition to residues nec essary for enzymatic function, those amino acids comprising structural ly important folding cores are also preferentially conserved during ev olution. This implies that the identified folding cores may be part of an array of fundamental structural folding units.