Structural basis of protein kinetic stability: resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward beta-sheet structure

Abstract

The term kinetic stability is used to describe proteins that are trapped in a specific conformation because of an unusually high-unfolding barrier that results in very slow unfolding rates. Motivated by the observation that some proteins are resistant to sodium dodecyl sulfate (SDS)-induced denaturation, an attempt was made to determine whether this property is a result of kinetic stability. We studied many proteins, including a few kinetically stable proteins known to be resistant to SDS. The resistance to SDS-induced denaturation was investigated by comparing the migration on polyacrylamide gels of identical boiled and unboiled protein samples containing SDS. On the basis of the different migration of these samples, eight proteins emerged as being resistant to SDS. The kinetic stability of these proteins was confirmed by their slow unfolding rate upon incubation in guanidine hydrochloride. Further studies showed that these proteins were also extremely resistant to proteolysis by proteinase K, suggesting that a common mechanism may account for their resistance to SDS and proteolytic cleavage. Together, these observations suggest that a rigid protein structure may be the physical basis for kinetic stability and that resistance to SDS may serve as a simple assay for identifying proteins whose native conformations are kinetically trapped. Remarkably, most of the kinetically stable SDS-resistant proteins in this study are oligomeric beta-sheet proteins, suggesting a bias of these types of structures toward kinetic stability.