Question

How long will it take the polypeptide backbone of a 6-residue folding nucleus to explore all its possible conformations? Repeat the calculation for 10-, 15-, and 20-residue folding nuclei. Why, in the classic view of protein folding, are folding nuclei thought to be no larger than 15 residues?

Answer 1

It will take the polypeptide backbone of a 6-residue chain to sample all possible confirmations ~ 6 ms (= 6*10^-3 s)

It will take the polypeptide backbone of a 10-residue chain to sample all possible confirmations ~ 10 ms

It will take the polypeptide backbone of a 15-residue chain to sample all possible confirmations ~ 15 ms

It will take the polypeptide backbone of a 20-residue chain to sample all possible confirmations ~ 20 ms

Explanation: In literature, it is reported that for 100-residue proteins, 3*10⁷ distinct topomers are found and it diffusively samples one topomer every ~ 3 ns (= 3*10^-9 s). Hence, a 100-residue protein can find its native topomer by random sampling in ~ 3*10⁷*3*10^-9 s ~ 10²*10^-3 s = 100 ms