The topomer-sampling model of protein folding

Clearly, a protein cannot sample all of its conformations (e.g., approximat e to 3(100) approximate to 10(48) for a 100 residue protein) on an in vivo folding timescale (<1 s), To investigate how the conformational dynamics of a protein can accommodate sub second folding time scales, we introduce the concept of the native topomer, which is the set of ail structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bondi ng of the peptide backbone). We hare developed a computational procedure fo r estimating the number of distinct topomers required to span all conformat ions (compact and semicompact) for a polypeptide of a gh en length, For 100 residues, we find approximate to 3 x 10(7) distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-res idue polypeptide diffusively samples one topomer every approximate to 3 ns. Hence, a 100-residue protein can find its native topomer by random samplin g in just approximate to 100 ms. These results suggest that subsecond foldi ng of modest-sized, single-domain proteins can be accomplished by a two-sta ge process of(il topomer diffusion: random, diffusive sampling of the 3 x 1 0(7) distinct topomers to find the native topomer (approximate to 0.1 s), f ollowed by iii) intratopomer ordering: nonrandom, local conformational rear rangements within the native topomer to settle into the precise native stat e.