Protein folding in the cell: reshaping the folding funnel

Models of protein folding have historically focused on a subset of 'well-behaved' proteins that can be successfully refolded from denaturants in vitro. Energy landscapes, including folding funnel 'cartoons', describe the largely uncomplicated folding of these isolated chains at infinite dilution. However, the frequent failure of many polypeptides to fold to their native state requires more comprehensive models of folding to accommodate the crucial role of interactions between partially folded intermediates. By incorporating additional deep minima, which reflect off-pathway interchain interactions, the folding funnel concept can be extended to describe the behavior of a more diverse set of proteins under more physiologically relevant conditions. In particular, the effects of ribosomes (translation), molecular chaperones and other aspects of the cellular environment on early chain conformations can be included to account for the folding behavior of polypeptide chains in cells.