Jump transition observed in translocation time for ideal poly-X proteinogenic chains as a result of competing folding and anchoraging contributions.

Abstract

In this work we analyze the translocation of homopolymer chains poly-X, where X represents any of the 20 naturally occurring amino acid residues, in terms of size N and single-helical propensity ω. We provide an analytical framework to calculate both the free energy F of translocation and the translocation time τ as a function of chain size N, energies U and ε of the unfolded and folded states, respectively. Our results show that free energy F has a characteristic bell-shaped barrier as function of the percentage of monomers translocated. Inclusion of single-helical propensity ω associated to monomer X and chain's native energy ε in the translocation model increases the energy barrier ΔF up to one order of magnitude as compared with the well-known Gaussian chain model. Computation of the mean first-passage time as function of chain size N shows that the translocation time τ exhibits a significant jump of several orders of magnitude at a critical chain size N. This jump markedly slows down translocation of chains larger than N. Existence of the transition jump of τ has been observed experimentally at least in poly(ethylene oxide) chains [R. P. Choudhury, P. Galvosas, and M. Schönhoff, J. Phys. Chem. B 112, 13245 (2008)]JPCBFK1520-610610.1021/jp804680q. Our results suggest the transition jump of τ as a function of N may be a very well spread feature throughout translocation of poly-X chains.