Nanopore–Protein Interactions Dramatically Alter Stability and Yield of the Native State in Restricted Spaces

We have studied the stability and the yield of the folded WW domains in a spherical nanopore to provide insights into the changes in the folding characteristics due to interactions of the polypeptide (SP) with the walls of the pore. Using different models for the interactions between the nanopore and the polypeptide chain we have obtained results that are relevant to a broad range of experiments. (a) In the temperature and the strength of the SP–pore interaction plane (λ), there are four “phases,” namely, the unfolded state, the native state, the molten globule phase (MG), and the surface interaction-stabilized (SIS) state. The MG and SIS states are populated at moderate and large values of λ, respectively. For a fixed pore size, the folding rates vary non-monotonically as λ is varied with a maximum at λ≈1 at which the SP–nanopore interaction is comparable to the stability of the native state. At large λ values, the WW domain is kinetically trapped in the SIS states. Using multiple sequence alignment, we conclude that similar folding mechanism should be observed in other WW domains as well. (b) To mimic the changes in the nature of the allosterically driven SP–GroEL interactions we consider two models for the dynamic Anfinsen cage (DAC). In DAC1, the SP–cavity interaction cycles between hydrophobic (λ>0) and hydrophilic (λ=0) with a period τ. The yield of the native state is a maximum for an optimum value of τ=τOPT. At τ=τOPT, the largest yield of the native state is obtained when τH≈τP where τH(τP) is the duration for which the cavity is hydrophobic (hydrophilic). Thus, in order to enhance the native state yield, the cycling rate, for a given loading rate of the GroEL nanomachine, should be maximized. In DAC2, the volume of the cavity is doubled (as happens when ATP and GroES bind to GroEL) and the SP–pore interaction simultaneously changes from hydrophobic to hydrophilic. In this case, we find greater increase in yield of the native state compared to DAC1 at all values of τ.