The topomer-sampling model of protein folding

摘要

Clearly, a protein cannot sample all of its conformations on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainabIe from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polyPeptide of a given length. For 100 residues, we find approximately equals 3 x 10(7) distinct topomers. Based on the distance calculated between different topomers, we estimate that a l00-residue polyPeptide diffesively samples one topomer every approximately equals 3 ns. Hence, a 100-residue protein can filld its native topomer by raudom sampling in just approximately 100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffesion: random, diffusive sampling of the 3 x 10(7) distinct topomers to find the native topomer ( approximately equals 0.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state.