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Time scale, geometrical constraints, and disulfide bond formation in the folding of small globular proteins

We hypothesize a model of protein folding based on the Poincaré recursion argument and a number of experimental results, including CD, nmr, and Raman spectra. Our model considers that protein folding in vivo proceeds through prefolded peptide segments consisting of 3 to 14 amino acid residues. Such segments may fold spontaneously into nativelike microdomains within a biologically feasible time, i.e., in the 10−6–10−1 s time scale. If, due to improper recognition and adjustment of their surfaces, these transiently formed secondary structures are not stabilized by long‐range interactions, then the protein species occur within a time‐ and number‐averaged spectrum of populations of transient conformational substates until the final, proper adjustment of the segments takes place. However, if, during protein folding, incorrect disulfide (S‐S) bonds are formed, then such unique through‐space contacts between the different parts of the polypeptide chain are usually restricted to a minimum. It is postulated that unfolding and refolding processes in vitro, and protein folding in vivo, proceed through variably populated quantized substates. The distribution of these substates depends on a number of molecular interactions between the phase and the hydration spheres surrounding the prefolded surfaces of peptide segments and long‐range interactions between these prefolded surfaces.