Protein engineering strategies in examining protein folding intermediates

How cooperative are protein folding and unfolding transitions?

A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.

Evidence for an obligatory intermediate in the folding of interleukin-1 beta

The folding of the beta-sheet protein, interleukin-1 beta, was examined at pH 5.0 and 25 degrees C using pulse-labelling hydrogen exchange and electrospray ionization mass spectrometric analysis, as well as stopped-flow circular dichroism and fluorescence spectroscopies. The first detectable event is the formation of a partially folded intermediate in a kinetic step with a relaxation time of 126 +/- 26 ms. There is a lag in native protein production of at least 400 ms. Optical studies indicate that the intermediate is converted to the native species in a reaction with a relaxation time of 43 +/- 5 s. The kinetic rates determined from stopped-flow fluorescence, circular dichroism and pulse-labelling experiments are similar and consistent with a simple sequential model for the folding pathway of interleukin-1 beta at pH 5.0 and 25 degrees C. Taken together, our data provide kinetic evidence that formation of the native state of interleukin-1 beta proceeds through an obligatory intermediate. We explain our results in terms of the classical and new views of protein folding.

NMR study of the reconstitution of the beta-sheet of thioredoxin by fragment complementation

The study of complementary protein fragments is thought to be generally useful to identify early folding intermediates. A prerequisite for these studies is the reconstitution of the native-like structure by fragment complementation. Structural analysis of the complementation of the domain-sized proteolytic fragments of E. coli thioredoxin, using a combination of H-exchange and 2D NMR experiments as a fingerprint technique, provide evidence for the extensive reconstitution of a native beta-sheet, with local conformational adjustments near the cleavage site. Remarkably, the antiparallel beta-strand between the fragments shows a native-like protection of the amide protons to solvent exchange. Our results indicate that these fragments can be useful to study the early events in the still little understood formation of beta-sheets.