The nature of protein folding pathways

Abstract

How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the "new view" model for protein folding. Emergent macroscopic foldon-foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the "how" and the "why" questions. The protein folding pathway depends on the same foldon units and foldon-foldon interactions that construct the native structure.protein folding | hydrogen exchange | protein structure

Defining the Apoptotic Trigger

“…In the partially unfolded state the heme prosthetic group gains the ability to act as a peroxidase that is apparently specific for CL (2). Titration of liposomes into dilute solutions of cytochrome c suggests the promotion of a subpopulation of partially unfolded species with increasing CL membrane content and CL:cytochrome c ratio (4), perhaps in accordance with the cooperative substructure of the protein revealed by an array of biophysical studies (5). These observations, however, present a paradox: considering the enrichment of CL in the mitochondrion, how does this mechanism not constantly result in a substantial fraction of unfolded cytochrome c in vivo, diminishing the ability of cytochrome c to shuttle electrons and potentially causing aberrant apoptosis signaling?…”

The case for defined protein folding pathways

“…The entire protein population folds the same segment first, all at the same rate, and all experience the same subsequent steps in the same order at the same rate, as suggested in The selection of native as opposed to nonnative interactions during folding is directed by a funnel-shaped energy landscape (80). (B) Experiment shows that, under equilibrium native conditions, cyt c unfolds by stepping energetically uphill through a ladder of forms that differ one from the next by the unfolding of one more native-like foldon (far right) (16,17). HX MS experiments during kinetic folding demonstrate a pathway that steps sequentially downhill through the same intermediates (40).…”

“…The discovery and study of protein foldons (15)(16)(17) point to a different folding mechanism, illustrated in Fig. 1B.…”

“…The numerous trajectories envisioned in the many-pathway model have been detected and characterized (18)(19)(20) and so can be considered on their merits rather than by abstract inference. Continued methods development (21,22) has enhanced the search for foldons and the investigation of their role in both equilibrium and kinetic folding (16,17). Advances in computational methods add a new vantage point (23)(24)(25)(26).…”

Long Range Polymer Chain Dynamics Studied by Fluorescence Quenching

“…Due to this inherent complexity, the characterization of the internal dynamics of biological macromolecules is a very active research area, in particular to determine the folding pathway of proteins. [7][8][9][10][11] The overarching goal in these studies is to determine the time taken for the folding of structural intermediates toward the ultimate 3-dimensional structure of the protein, a process that would benefit from the characterization of the internal dynamics of individual polypeptide chains in solution. As a result, techniques capable of probing polymer chain dynamics in solution have attracted strong scientific interest.…”