Unifying features in protein-folding mechanisms

Abstract

We compare the folding of representative members of a protein superfamily by experiment and simulation to investigate common features in folding mechanisms. The homeodomain superfamily of three-helical, single-domain proteins exhibits a spectrum of folding processes that spans the complete transition from concurrent secondary and tertiary structure formation (nucleation-condensation mechanism) to sequential secondary and tertiary formation (framework mechanism). The unifying factor in their mechanisms is that the transition state for (un)folding is expanded and very native-like, with the proportion and degree of formation of secondary and tertiary interactions varying. There is a transition, or slide, from the framework to nucleation-condensation mechanism with decreasing stability of the secondary structure. Thus, framework and nucleation-condensation are different manifestations of an underlying common mechanism.two-state ͉ three-state ͉ framework ͉ nucleation ͉ homeodomain A Holy Grail of protein folding is to find a single mechanism. Given the diversity of protein structure and the evolutionary pressure on function and not on folding rates, a unique mechanism for folding would seem unlikely. If there are simplifying features, then small, single-domain proteins may be the most likely to exhibit them. But such proteins seem to fold by two distinct mechanisms. The 6-85 repressor fragment (1) and the engrailed homeodomain (En-HD; ref.2) seem to fold by a classical diffusion-collision mechanism (3-5) whereby secondary structural elements form independently and then dock to form the tertiary structure. Chymotrypsin inhibitor 2, on the other hand, folds by nucleation-condensation, which is characterized by concerted consolidation of secondary and tertiary interactions as the whole domain collapses around an extended nucleus (6). It has been argued on general grounds that nucleation-condensation and diffusion-collision are different manifestations of a common mechanism in which secondary structure and tertiary structure form in parallel (7,8). Nucleationcondensation reflects the situation when secondary structure is inherently unstable in the absence of tertiary interactions whereas diffusion-collision becomes more probable with increasing stability of secondary structure.Studies of the folding of point mutants of a prototype protein are essential for discovering atomic level details of folding mechanisms and kinetics. Single-point mutants may even cause gross changes in the kinetics of folding, such as the transition from three-state to two-state folding (9). But, to extrapolate a general understanding of folding mechanisms, studies on members of the same fold family (different homologues sharing the same overall topology but with different primary structures) can be useful in finding correlations between amino acid sequences and three-dimensional structures (10-16). Although there can be different folding routes through different transition states for some proteins (17), it seems that mechanisms of folding are oft...

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

“…The two different classes of pathways are reminiscent of the two prevalent generic protein folding mechanisms, the diffusion-collision mechanism (1) and the nucleation-condensation mechanism (2). Our results indicate that both mechanisms can act simultaneously in one protein (3,17). Another finding of this work is the existence of a long-lived partly solvated intermediate on the NI path, the P d state, characterized by a detached proline.…”

“…In the nucleation-condensation mechanism (2), a nucleus of crucial tertiary contacts is made, around which the native structure condensates. In recent years, these two mechanisms were combined in a unified view (3).…”

Molecular dynamics and protein function

“…In the former model, the helices form first and then diffuse to find the native fold [a limiting case of the diffusion-collision model (21)], whereas, in the latter model, there first is a collapse to a relatively disordered globule and the helices form simultaneously with the native tertiary structure. The model results correlate with recent folding experiments and all-atom (unfolding) simulations in explicit solvent (22). Interestingly, an extension of the discrete dynamics methodology has recently been used to simulate fibril formation from random coil peptides, illustrating a possible mechanism by which large, relatively well ordered ␤-sheet aggregates could appear in solution (23).…”

Identification and characterization of protein folding intermediates

“…[58]. These observations indicate that, as observed in the case of cytochrome c [59], apo-myoglobin [16], the PDZ domain [60] and homeodomain-like superfamilies [6,7], intermediate formation is a general step in immunity protein folding and suggest that it is necessary to explore a wide range of refolding conditions in order to show that intermediates do or do not form.…”

“…The two state mechanism provided the basis for a nucleation-condensation mechanism, with folding through simultaneous formation of secondary and tertiary structure centered around a small folding nucleus [4,5]. Recent work on the homeodomain superfamily [6,7] and on a PDZ domain [8], led to the view that the framework and nucleation-condensation models represent extreme manifestation of an underlying common mechanism and that proteins may appear to fold by either the nucleation-condensation or framework mechanism depending on the inherent stability of their secondary structure elements [7,9].…”