Reconfiguration dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant.

We consider a flexible chain with internal friction in a harmonic confinement and extend it to include the effects of solvent quality at the mean field level by introducing a Flory type exponent ν . The strength of the harmonic confinement ( k c ) accounts for the denaturant concentration and connects to the internal friction of the chain ( ξ i n t ) through an ansatz. Our calculated reconfiguration times falling in the range of 5–50 ns are found out to be within 10%–15% of the experimentally measured reconfiguration times of the folded cold shock protein and the intrinsically disordered protein prothymosin α . In addition, our calculations show that the reconfiguration time scales with the chain length N as ∼ N α , where α depends weakly on the internal friction but has rather stronger dependence on the solvent quality. In the absence of any internal friction, α = 2 ν + 1 and it goes down in the presence of internal friction, but chain reconfiguration slows down in general. On the contrary, in a poorer solvent chain reconfiguration and looping become faster even though the internal friction is higher in the collapsed state. [ABSTRACT FROM AUTHOR]